Start: 2026-02-28 05:42:21 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 --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --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 1.6.1~202508211856~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --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-ubc-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/tmp149xq_no 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp149xq_no 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp149xq_no', '--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/tmp149xq_no', '--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/tmp149xq_no/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp149xq_no/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/tmp149xq_no/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/tmp149xq_no/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp149xq_no/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 to /srv/piuparts.debian.org/tmp/tmp149xq_no/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmp149xq_no/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'update'] 0m1.4s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 33c7e74460b374c64edf181f36fe234c - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s 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 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_fake-essential'] 0m5.3s DUMP: *** Adding fake essential packages *** Reading package lists... Building dependency tree... init-system-helpers is already the newest version (1.69). Solving dependencies... The following additional packages will be installed: libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf Suggested packages: dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks Recommended packages: libgpm2 psmisc linux-sysctl-defaults The following NEW packages will be installed: dbconfig-common libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps sensible-utils ucf 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 1779 kB of archives. After this operation, 4989 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b5 [9532 B] Get:6 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:7 http://deb.debian.org/debian sid/main amd64 ucf all 3.0052 [43.3 kB] Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.25 [604 kB] Preconfiguring packages ... Fetched 1779 kB in 1s (3508 kB/s) Selecting previously unselected package libncursesw6: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 ... 4900 files and directories currently installed.) Preparing to unpack .../0-libncursesw6_6.6+20251231-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.6+20251231-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../1-libproc2-0_2%3a4.0.4-9+b1_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9+b1) ... Selecting previously unselected package procps. Preparing to unpack .../2-procps_2%3a4.0.4-9+b1_amd64.deb ... Unpacking procps (2:4.0.4-9+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../3-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libtext-charwidth-perl:amd64. Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b5_amd64.deb ... Unpacking libtext-charwidth-perl:amd64 (0.04-11+b5) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../5-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../6-ucf_3.0052_all.deb ... Moving old data out of the way Unpacking ucf (3.0052) ... Selecting previously unselected package dbconfig-common. Preparing to unpack .../7-dbconfig-common_2.0.25_all.deb ... Unpacking dbconfig-common (2.0.25) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b5) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libproc2-0:amd64 (2:4.0.4-9+b1) ... Setting up libncursesw6:amd64 (6.6+20251231-1) ... Setting up sensible-utils (0.0.26) ... Setting up procps (2:4.0.4-9+b1) ... Setting up ucf (3.0052) ... Setting up dbconfig-common (2.0.25) ... Creating config file /etc/dbconfig-common/config with new version Processing triggers for libc-bin (2.42-13) ... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_fake-essential'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_forbid_home'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.3s 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' 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_minimize'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_minimize'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_zz_backports'] 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_setup_zz_backports'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 0m5.4s DEBUG: Recording chroot state 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.9s 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 dbconfig-common dbconfig-common 2.0.25 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 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 libproc2-0:amd64 libproc2-0 2:4.0.4-9+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 libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 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 procps procps 2:4.0.4-9+b1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.26 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 ucf ucf 3.0052 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 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-divert', '--list'] 0m5.9s 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 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-divert', '--list'] 0m5.9s INFO: Running scripts is_testable 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/is_testable_uninstallable'] 0m5.9s INFO: apt-cache does not know about any of the requested packages 0m5.9s INFO: Running scripts pre_test 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_test_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_test_root_password'] 0m6.0s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_test_root_password'] 0m6.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m6.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m6.7s DEBUG: No broken symlinks as far as we can find. 0m6.7s INFO: Running scripts pre_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra=0.29.1-4'] 0m7.7s DUMP: 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-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_0.29.1-4_amd64.deb Size: 1118236 MD5sum: 869c747f56f90d091557112d30b8745b SHA256: a2794d871a590990b4e75a0eedfe7e2c9cc422940a9fd78c610765555b604c84 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra=0.29.1-4'] 0m7.7s DEBUG: metapackage: Package: piuparts-depends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: piuparts developers team 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 Description: Dummy package to satisfy dependencies - created by piuparts This package was created automatically by piuparts and can safely be removed 0m7.7s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpvjyzasq6/piuparts-depends-dummy'] 0m7.7s DUMP: dpkg-deb: warning: not checking contents of control area dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpvjyzasq6/piuparts-depends-dummy.deb'. 0m7.7s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpvjyzasq6/piuparts-depends-dummy'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m7.7s DUMP: 3.1.16 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt'] 0m7.7s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpvjyzasq6/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmp149xq_no/tmp 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m41.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40 libgomp1 liblapack3 libltdl7 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-trio python3-aioquic python-mpmath-doc python3-gmpy2 python3-matplotlib 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: 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 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 libsuitesparseconfig7 libxml2-16 media-types netbase openssl piuparts-depends-dummy 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 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 53.7 MB/53.7 MB of archives. After this operation, 274 MB of additional disk space will be used. Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy amd64 0.invalid.0 [762 B] Get:2 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 media-types all 14.0.0 [30.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 netbase all 6.5 [12.4 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 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-depinfo amd64 2.2.0-4 [11.7 kB] Get:40 http://deb.debian.org/debian sid/main amd64 python3-diskcache all 5.6.3-1 [34.4 kB] Get:41 http://deb.debian.org/debian sid/main amd64 python3-dnspython all 2.7.0-1 [164 kB] Get:42 http://deb.debian.org/debian sid/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB] Get:43 http://deb.debian.org/debian sid/main amd64 python3-h11 all 0.14.0-1.1 [50.6 kB] Get:44 http://deb.debian.org/debian sid/main amd64 python3-httpcore all 1.0.9-1 [45.0 kB] Get:45 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.19.2+dfsg-1 [847 kB] Get:46 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get:47 http://deb.debian.org/debian sid/main amd64 python3-uc-micro all 1.0.3-1 [5744 B] Get:48 http://deb.debian.org/debian sid/main amd64 python3-linkify-it all 2.0.3-2 [18.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-3 [59.5 kB] Get:50 http://deb.debian.org/debian sid/main amd64 python3-rich all 13.9.4-1.2 [203 kB] Get:51 http://deb.debian.org/debian sid/main amd64 python3-httpx all 0.28.1-1 [76.2 kB] Get:52 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.4.0-1 [448 kB] Get:53 http://deb.debian.org/debian sid/main amd64 python3-swiglpk amd64 5.0.10-2+b3 [92.5 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-optlang all 1.8.3-1 [5375 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.2-5 [31.8 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6583 kB] Get:58 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.3.3+dfsg-3 [2935 kB] Get:59 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.9.2-1 [18.4 kB] Get:60 http://deb.debian.org/debian sid/main amd64 python3-pydantic-core amd64 2.41.5-2+b1 [2193 kB] Get:61 http://deb.debian.org/debian sid/main amd64 python3-typing-inspection all 0.4.2-1 [13.8 kB] Get:62 http://deb.debian.org/debian sid/main amd64 python3-pydantic amd64 2.12.5-2 [380 kB] Get:63 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.15+ds-1 [181 kB] Get:64 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get:65 http://deb.debian.org/debian sid/main amd64 python3-sbml5 amd64 5.20.5+dfsg-3 [3534 kB] Get:66 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Preconfiguring packages ... Fetched 53.7 MB in 2s (22.0 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 ... 5441 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 ... 5775 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.9-3_amd64.deb ... Unpacking python3-minimal (3.13.9-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../3-libffi8_3.5.2-3+b1_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-3+b1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.3-4_all.deb ... Unpacking readline-common (8.3-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.3-4_amd64.deb ... 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 .../6-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 .../7-libpython3.13-stdlib_3.13.12-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.12-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.12-1_amd64.deb ... Unpacking python3.13 (3.13.12-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.9-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.9-3) ... Setting up python3-minimal (3.13.9-3) ... Selecting previously unselected package python3. (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 ... 6283 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.9-3_amd64.deb ... Unpacking python3 (3.13.9-3) ... Selecting previously unselected package python3-numpy-dev:amd64. Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../02-libblas3_3.12.1-7+b1_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-7+b1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../03-libgfortran5_15.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (15.2.0-14) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../04-liblapack3_3.12.1-7+b1_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-7+b1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... Unpacking python3-numpy (1:2.3.5+ds-3) ... Selecting previously unselected package openssl. Preparing to unpack .../06-openssl_3.5.5-1_amd64.deb ... Unpacking openssl (3.5.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../07-ca-certificates_20260223_all.deb ... Unpacking ca-certificates (20260223) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../08-libgomp1_15.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (15.2.0-14) ... Selecting previously unselected package libsuitesparseconfig7:amd64. Preparing to unpack .../09-libsuitesparseconfig7_1%3a7.12.2+dfsg-1_amd64.deb ... Unpacking libsuitesparseconfig7:amd64 (1:7.12.2+dfsg-1) ... Selecting previously unselected package libamd3:amd64. Preparing to unpack .../10-libamd3_1%3a7.12.2+dfsg-1_amd64.deb ... Unpacking libamd3:amd64 (1:7.12.2+dfsg-1) ... Selecting previously unselected package libcolamd3:amd64. Preparing to unpack .../11-libcolamd3_1%3a7.12.2+dfsg-1_amd64.deb ... Unpacking libcolamd3:amd64 (1:7.12.2+dfsg-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../12-libltdl7_2.5.4-9_amd64.deb ... Unpacking libltdl7:amd64 (2.5.4-9) ... Selecting previously unselected package libglpk40:amd64. Preparing to unpack .../13-libglpk40_5.0-2+b1_amd64.deb ... Unpacking libglpk40:amd64 (5.0-2+b1) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../14-libpython3.13_3.13.12-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.12-1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../15-libxml2-16_2.15.1+dfsg-2+b1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Selecting previously unselected package python-cobra-data. Preparing to unpack .../16-python-cobra-data_0.29.1-4_all.deb ... Unpacking python-cobra-data (0.29.1-4) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../17-python3-typing-extensions_4.15.0-2_all.deb ... Unpacking python3-typing-extensions (4.15.0-2) ... Selecting previously unselected package python3-annotated-types. Preparing to unpack .../18-python3-annotated-types_0.7.0-1_all.deb ... Unpacking python3-annotated-types (0.7.0-1) ... Selecting previously unselected package python3-idna. Preparing to unpack .../19-python3-idna_3.11-1_all.deb ... Unpacking python3-idna (3.11-1) ... Selecting previously unselected package python3-anyio. Preparing to unpack .../20-python3-anyio_4.12.1-1_all.deb ... Unpacking python3-anyio (4.12.1-1) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../21-python3-certifi_2026.2.25+ds-1_all.deb ... Unpacking python3-certifi (2026.2.25+ds-1) ... Selecting previously unselected package python3-click. Preparing to unpack .../22-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../23-python3-dateutil_2.9.0-4_all.deb ... Unpacking python3-dateutil (2.9.0-4) ... Selecting previously unselected package python3-depinfo. Preparing to unpack .../24-python3-depinfo_2.2.0-4_amd64.deb ... Unpacking python3-depinfo (2.2.0-4) ... 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-dnspython. Preparing to unpack .../26-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 .../27-python3-email-validator_2.2.0-1_all.deb ... Unpacking python3-email-validator (2.2.0-1) ... Selecting previously unselected package python3-h11. Preparing to unpack .../28-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 .../29-python3-httpcore_1.0.9-1_all.deb ... Unpacking python3-httpcore (1.0.9-1) ... Selecting previously unselected package python3-pygments. Preparing to unpack .../30-python3-pygments_2.19.2+dfsg-1_all.deb ... Unpacking python3-pygments (2.19.2+dfsg-1) ... Selecting previously unselected package python3-mdurl. Preparing to unpack .../31-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 .../32-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 .../33-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 .../34-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 .../35-python3-rich_13.9.4-1.2_all.deb ... Unpacking python3-rich (13.9.4-1.2) ... Selecting previously unselected package python3-httpx. Preparing to unpack .../36-python3-httpx_0.28.1-1_all.deb ... Unpacking python3-httpx (0.28.1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../37-python3-mpmath_1.4.0-1_all.deb ... Unpacking python3-mpmath (1.4.0-1) ... Selecting previously unselected package python3-swiglpk. Preparing to unpack .../38-python3-swiglpk_5.0.10-2+b3_amd64.deb ... Unpacking python3-swiglpk (5.0.10-2+b3) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../39-python3-sympy_1.14.0-2_all.deb ... Unpacking python3-sympy (1.14.0-2) ... Selecting previously unselected package python3-optlang. Preparing to unpack .../40-python3-optlang_1.8.3-1_all.deb ... Unpacking python3-optlang (1.8.3-1) ... Selecting previously unselected package python3-pytz. Preparing to unpack .../41-python3-pytz_2025.2-5_all.deb ... Unpacking python3-pytz (2025.2-5) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../42-python3-pandas-lib_2.3.3+dfsg-3_amd64.deb ... Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../43-python3-pandas_2.3.3+dfsg-3_all.deb ... Unpacking python3-pandas (2.3.3+dfsg-3) ... Selecting previously unselected package python3-platformdirs. Preparing to unpack .../44-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 .../45-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 .../46-python3-typing-inspection_0.4.2-1_all.deb ... Unpacking python3-typing-inspection (0.4.2-1) ... Selecting previously unselected package python3-pydantic. Preparing to unpack .../47-python3-pydantic_2.12.5-2_amd64.deb ... Unpacking python3-pydantic (2.12.5-2) ... Selecting previously unselected package python3-ruamel.yaml.clib. Preparing to unpack .../48-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 .../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-sbml5. Preparing to unpack .../50-python3-sbml5_5.20.5+dfsg-3_amd64.deb ... Unpacking python3-sbml5 (5.20.5+dfsg-3) ... Selecting previously unselected package python3-tabulate. Preparing to unpack .../51-python3-tabulate_0.9.0-1_all.deb ... Unpacking python3-tabulate (0.9.0-1) ... Selecting previously unselected package piuparts-depends-dummy. Preparing to unpack .../52-piuparts-depends-dummy.deb ... Unpacking piuparts-depends-dummy (0.invalid.0) ... 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 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 piuparts-depends-dummy (0.invalid.0) ... 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. 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb'] 0m41.3s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok 0m41.3s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmp149xq_no/./tmp/piuparts-depends-dummy.deb 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m41.3s DUMP: piuparts-depends-dummy install ok installed 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m41.3s DUMP: (Reading database ... 13135 files and directories currently installed.) Removing piuparts-depends-dummy (0.invalid.0) ... 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'piuparts-depends-dummy'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 0m41.4s DEBUG: Recording chroot state 0m42.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m43.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m44.6s DEBUG: No broken symlinks as far as we can find. 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m45.4s 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: 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m45.4s 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 0m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m47.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Suggested packages: python3-matplotlib qsopt-ex The following NEW packages will be installed: python3-cobra 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1118 kB of archives. After this operation, 1921 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 python3-cobra amd64 0.29.1-4 [1118 kB] Fetched 1118 kB in 1s (1618 kB/s) Selecting previously unselected package python3-cobra. (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 ... 13135 files and directories currently installed.) Preparing to unpack .../python3-cobra_0.29.1-4_amd64.deb ... Unpacking python3-cobra (0.29.1-4) ... Setting up python3-cobra (0.29.1-4) ... 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m47.2s INFO: Running scripts post_install 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'systemd-tmpfiles', '--cat-config'] 0m47.2s DUMP: chroot: failed to run command 'systemd-tmpfiles': No such file or directory 0m47.2s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'systemd-tmpfiles', '--cat-config'] 0m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'remove', 'python3-cobra'] 0m48.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following packages were automatically installed and are no longer required: libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40 libgomp1 liblapack3 libltdl7 libpython3-stdlib libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0 libsuitesparseconfig7 libxml2-16 media-types netbase 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 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: python3-cobra 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 1921 kB 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 ... 13234 files and directories currently installed.) Removing python3-cobra (0.29.1-4) ... 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'remove', 'python3-cobra'] 0m48.1s INFO: Reinstalling after remove 0m48.1s INFO: Running scripts pre_install 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m48.2s 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: 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m48.3s 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 0m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m49.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Suggested packages: python3-matplotlib qsopt-ex The following NEW packages will be installed: python3-cobra 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/1118 kB of archives. After this operation, 1921 kB of additional disk space will be used. Selecting previously unselected package python3-cobra. (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 ... 13135 files and directories currently installed.) Preparing to unpack .../python3-cobra_0.29.1-4_amd64.deb ... Unpacking python3-cobra (0.29.1-4) ... Setting up python3-cobra (0.29.1-4) ... 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-4'] 0m49.4s INFO: Running scripts post_install 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m49.4s INFO: Running scripts pre_install 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_database-server'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_exceptions'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_extras'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m49.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m49.5s DUMP: python3-cobra: Installed: 0.29.1-4 Candidate: 0.29.1-4 Version table: *** 0.29.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m49.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-cache', 'policy', 'python3-cobra'] 0m49.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', '--reinstall', 'python3-cobra=0.29.1-4'] 0m50.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... 0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/1118 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 13234 files and directories currently installed.) Preparing to unpack .../python3-cobra_0.29.1-4_amd64.deb ... Unpacking python3-cobra (0.29.1-4) over (0.29.1-4) ... Setting up python3-cobra (0.29.1-4) ... 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', '-y', 'install', '--reinstall', 'python3-cobra=0.29.1-4'] 0m50.8s INFO: Running scripts post_install 0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_install_exceptions'] 0m50.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m52.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 0m53.5s DEBUG: No broken symlinks as far as we can find. 0m54.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp149xq_no', '-ac', '--ignore-obsolete'] 0m56.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp149xq_no', '-ac', '--ignore-obsolete'] 0m56.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.1s DUMP: 0.15.9~deb12u1 0m56.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m56.1s INFO: Running adequate version 0.15.9~deb12u1 now. 0m56.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'python3-cobra'] 0m56.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'python3-cobra'] 0m56.2s INFO: Running scripts pre_remove 0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m56.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_exceptions'] 0m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_exceptions'] 0m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/pre_remove_preseed_cleanup'] 0m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.5s 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 dbconfig-common dbconfig-common 2.0.25 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 libproc2-0:amd64 libproc2-0 2:4.0.4-9+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 libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b5 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10 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 procps procps 2:4.0.4-9+b1 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 sensible-utils sensible-utils 0.0.26 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 ucf ucf 3.0052 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 0m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', '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', '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'] 1m3.3s 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 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, 66 to remove and 0 not upgraded. After this operation, 276 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 ... 13234 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 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) ... 1m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', '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', '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'] 1m3.3s INFO: Running scripts post_remove 1m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_remove_cleanup'] 1m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_remove_cleanup'] 1m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_remove_exceptions'] 1m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_remove_exceptions'] 1m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7: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'] 1m3.5s DUMP: (Reading database ... 5451 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 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) ... 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'liblapack3:amd64', 'libltdl7: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'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'python3-cobra'] 1m3.5s DUMP: dpkg: warning: ignoring request to remove python3-cobra which is not installed 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', 'python3-cobra'] 1m3.5s INFO: Running scripts post_purge 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_purge_exceptions'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_purge_exceptions'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_purge_manual_cleanup'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_purge_manual_cleanup'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', '--pending'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--purge', '--pending'] 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--remove', '--pending'] 1m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg', '--remove', '--pending'] 1m3.5s INFO: Running scripts post_test 1m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_test_exceptions'] 1m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'tmp/scripts/post_test_exceptions'] 1m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 1m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 1m4.4s DEBUG: No broken symlinks as far as we can find. 1m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-divert', '--list'] 1m4.4s 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 1m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'dpkg-divert', '--list'] 1m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 1m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp149xq_no', 'apt-get', 'clean'] 1m4.4s DEBUG: Recording chroot state 1m5.6s INFO: PASS: Installation and purging test. 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/shm'] 1m6.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/shm'] 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/console'] 1m6.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/console'] 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/ptmx'] 1m6.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/ptmx'] 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/pts'] 1m6.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/dev/pts'] 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/proc'] 1m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp149xq_no/proc'] 1m6.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 1m6.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp149xq_no'] 1m6.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp149xq_no 1m6.3s INFO: PASS: All tests. 1m6.3s INFO: piuparts run ends. ret=0 End: 2026-02-28 05:43:27 GMT