Start: 2025-03-17 14:13:59 GMT
Package: python3-cobra
Source: python-cobra
Version: 0.29.1-1
Installed-Size: 1877
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-importlib-resources, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-1), python3-tabulate, python3-sbml5
Suggests: python3-matplotlib, qsopt-ex
Description: constraint-based modeling of biological networks with Python 3
Homepage: https://opencobra.github.io/cobrapy/
Description-md5: 0052f98776eccb61924a15b5d6618e25
Section: python
Priority: optional
Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-1_amd64.deb
Size: 1119236
MD5sum: 4d48b6813dbb603a20ea4fd8ad145ff3
SHA256: ef5f54c3547145e50a549a78b4977494290bf100e2b7fe34480c5a0b4386eab2
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=0.29.1-1
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 1.5.2~202503162239~1.5.1-10-g345d5865 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=0.29.1-1
0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64
0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpxaao9g9n
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpxaao9g9n
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/proc']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/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/tmpxaao9g9n/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/tmpxaao9g9n/dev/pts']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/ptmx']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/ptmx']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/console']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/8', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/console']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/shm']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/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/tmpxaao9g9n/tmp/scripts/
0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpxaao9g9n/tmp/scripts/
0m0.4s INFO: Running scripts post_chroot_unpack
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'update']
0m3.4s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7385 kB]
Fetched 17.7 MB in 2s (9206 kB/s)
Reading package lists...
0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'update']
0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-yf', 'dist-upgrade']
0m4.8s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
The following packages will be upgraded:
libselinux1 libsemanage-common libsemanage2 libsepol2 login.defs passwd
6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 1898 kB of archives.
After this operation, 9216 B of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.17.3-2 [186 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.8.1-1 [7812 B]
Get:4 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.8.1-1 [296 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.8.1-1 [95.3 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.17.3-2 [1228 kB]
Fetched 1898 kB in 0s (37.1 MB/s)
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Preparing to unpack .../libselinux1_3.8.1-1_amd64.deb ...
Unpacking libselinux1:amd64 (3.8.1-1) over (3.8-4) ...
Setting up libselinux1:amd64 (3.8.1-1) ...
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Preparing to unpack .../login.defs_1%3a4.17.3-2_all.deb ...
Unpacking login.defs (1:4.17.3-2) over (1:4.17.3-1) ...
Preparing to unpack .../libsemanage-common_3.8.1-1_all.deb ...
Unpacking libsemanage-common (3.8.1-1) over (3.8-1) ...
Preparing to unpack .../libsepol2_3.8.1-1_amd64.deb ...
Unpacking libsepol2:amd64 (3.8.1-1) over (3.8-1) ...
Preparing to unpack .../libsemanage2_3.8.1-1_amd64.deb ...
Unpacking libsemanage2:amd64 (3.8.1-1) over (3.8-1+b1) ...
Preparing to unpack .../passwd_1%3a4.17.3-2_amd64.deb ...
Unpacking passwd (1:4.17.3-2) over (1:4.17.3-1) ...
Setting up login.defs (1:4.17.3-2) ...
Setting up libsemanage-common (3.8.1-1) ...
Setting up libsepol2:amd64 (3.8.1-1) ...
Setting up libsemanage2:amd64 (3.8.1-1) ...
Setting up passwd (1:4.17.3-2) ...
Processing triggers for libc-bin (2.41-6) ...
0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-yf', 'dist-upgrade']
0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m5.2s DUMP:
0582dbe94023bf6cf8b7d535b964b205 -
0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m5.2s INFO: Running scripts post_setup
0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_dummy_users']
0m6.1s DUMP:
useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999
useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999
useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999
useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999
useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999
useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999
useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999
useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999
useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999
useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999
useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999
0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_dummy_users']
0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_fake-essential']
0m7.4s DUMP:
*** Adding fake essential packages ***
Reading package lists...
Building dependency tree...
Reading state information...
init-system-helpers is already the newest version (1.68).
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 1757 kB of archives.
After this operation, 4946 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 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 3.0050 [42.7 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB]
Preconfiguring packages ...
Fetched 1757 kB in 0s (26.8 MB/s)
Selecting previously unselected package libncursesw6:amd64.
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(Reading database ... 4907 files and directories currently installed.)
Preparing to unpack .../0-libncursesw6_6.5+20250216-2_amd64.deb ...
Unpacking libncursesw6:amd64 (6.5+20250216-2) ...
Selecting previously unselected package libproc2-0:amd64.
Preparing to unpack .../1-libproc2-0_2%3a4.0.4-7_amd64.deb ...
Unpacking libproc2-0:amd64 (2:4.0.4-7) ...
Selecting previously unselected package procps.
Preparing to unpack .../2-procps_2%3a4.0.4-7_amd64.deb ...
Unpacking procps (2:4.0.4-7) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libtext-charwidth-perl:amd64.
Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b4_amd64.deb ...
Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ...
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_3.0050_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0050) ...
Selecting previously unselected package dbconfig-common.
Preparing to unpack .../7-dbconfig-common_2.0.24_all.deb ...
Unpacking dbconfig-common (2.0.24) ...
Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ...
Setting up libtext-wrapi18n-perl (0.06-10) ...
Setting up libproc2-0:amd64 (2:4.0.4-7) ...
Setting up libncursesw6:amd64 (6.5+20250216-2) ...
Setting up sensible-utils (0.0.24) ...
Setting up procps (2:4.0.4-7) ...
Setting up ucf (3.0050) ...
Setting up dbconfig-common (2.0.24) ...
Creating config file /etc/dbconfig-common/config with new version
Processing triggers for libc-bin (2.41-6) ...
0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_fake-essential']
0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_forbid_home']
0m7.4s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_forbid_home']
0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.5s 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'
0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_minimize']
0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_minimize']
0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_squeeze-backports']
0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_squeeze-backports']
0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_zz_backports']
0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_setup_zz_backports']
0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m7.5s DEBUG: Recording chroot state
0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m8.0s DUMP:
install ok installed apt apt 2.9.33
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1+b1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed dbconfig-common dbconfig-common 2.0.24
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.18
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.33
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-2
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsystemd0:amd64 libsystemd0 257.4-3
install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4
install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.4-3
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-2
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.40.4-5
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-2
install ok installed perl-base perl-base 5.40.1-2
install ok installed procps procps 2:4.0.4-7
install ok installed sed sed 4.9-2
install ok installed sensible-utils sensible-utils 0.0.24
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed ucf ucf 3.0050
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-divert', '--list']
0m8.1s 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
0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-divert', '--list']
0m8.1s INFO: Running scripts is_testable
0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/is_testable_uninstallable']
0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/is_testable_uninstallable']
0m8.1s INFO: apt-cache does not know about any of the requested packages
0m8.1s INFO: Running scripts pre_test
0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_test_exceptions']
0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_test_exceptions']
0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_test_root_password']
0m8.1s DUMP:
New password: Retype new password: passwd: password updated successfully
0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_test_root_password']
0m8.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m8.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m9.0s DEBUG: No broken symlinks as far as we can find.
0m9.0s INFO: Running scripts pre_install
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra=0.29.1-1']
0m9.9s DUMP:
Package: python3-cobra
Source: python-cobra
Version: 0.29.1-1
Installed-Size: 1877
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-importlib-resources, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-1), python3-tabulate, python3-sbml5
Suggests: python3-matplotlib, qsopt-ex
Description-en: constraint-based modeling of biological networks with Python 3
COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
used for genome-scale modeling of metabolic networks in both prokaryotes
and eukaryotes. COBRApy is a constraint-based modeling package that is
designed to accommodate the biological complexity of the next generation
of COBRA models and provides access to commonly used COBRA methods, such
as flux balance analysis, flux variability analysis, and gene deletion
analyses.
Description-md5: 0052f98776eccb61924a15b5d6618e25
Homepage: https://opencobra.github.io/cobrapy/
Section: python
Priority: optional
Filename: pool/main/p/python-cobra/python3-cobra_0.29.1-1_amd64.deb
Size: 1119236
MD5sum: 4d48b6813dbb603a20ea4fd8ad145ff3
SHA256: ef5f54c3547145e50a549a78b4977494290bf100e2b7fe34480c5a0b4386eab2
0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'show', '--no-all-versions', 'python3-cobra=0.29.1-1']
0m9.9s DEBUG: metapackage:
Package: piuparts-depends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: piuparts developers team <piuparts-devel@alioth-lists.debian.net>
Depends: python3-depinfo, python3-diskcache, python3-httpx, python3-importlib-resources, python3-numpy, python3-optlang (>= 1.7.0-1~), python3-pandas, python3-platformdirs, python3-pydantic, python3-rich, python3-ruamel.yaml, python3-swiglpk (>= 5.0.8-1~), python3:any, python-cobra-data (= 0.29.1-1), python3-tabulate, python3-sbml5
Description: Dummy package to satisfy dependencies - created by piuparts
This package was created automatically by piuparts and can safely be removed
0m9.9s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpzyoilk2f/piuparts-depends-dummy']
0m9.9s DUMP:
dpkg-deb: warning: not checking contents of control area
dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmpzyoilk2f/piuparts-depends-dummy.deb'.
0m9.9s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmpzyoilk2f/piuparts-depends-dummy']
0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt']
0m9.9s DUMP:
2.9.33
0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt']
0m9.9s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmpzyoilk2f/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpxaao9g9n/tmp
0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb']
0m37.0s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5
libglpk40 libgomp1 libicu76 liblapack3 libltdl7 libpython3-stdlib
libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 libsuitesparseconfig7 libxml2 media-types netbase openssl
python-cobra-data python3 python3-annotated-types python3-anyio
python3-certifi python3-click python3-dateutil python3-depinfo
python3-diskcache python3-dnspython python3-email-validator python3-h11
python3-httpcore python3-httpx python3-idna python3-importlib-resources
python3-markdown-it python3-mdurl python3-minimal python3-mpmath
python3-numpy python3-numpy-dev python3-optlang python3-pandas
python3-pandas-lib python3-platformdirs python3-pydantic
python3-pydantic-core python3-pygments python3-pytz python3-rich
python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio
python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions
python3-tz 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 libicu76 liblapack3 libltdl7 libpython3-stdlib
libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 libsuitesparseconfig7 libxml2 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-importlib-resources
python3-markdown-it python3-mdurl python3-minimal python3-mpmath
python3-numpy python3-numpy-dev python3-optlang python3-pandas
python3-pandas-lib python3-platformdirs python3-pydantic
python3-pydantic-core python3-pygments python3-pytz python3-rich
python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio
python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions
python3-tz python3.13 python3.13-minimal readline-common
0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded.
Need to get 57.8 MB/57.8 MB of archives.
After this operation, 273 MB of additional disk space will be used.
Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy amd64 0.invalid.0 [778 B]
Get:2 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.2-2 [859 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.0-1 [107 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.2-2 [2210 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 media-types all 13.0.0 [29.3 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 3.4.7-1 [23.9 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-2 [913 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [1952 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.2-2 [746 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [138 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5084 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libsuitesparseconfig7 amd64 1:7.10.1+dfsg-1 [32.3 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libamd3 amd64 1:7.10.1+dfsg-1 [49.2 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libcolamd3 amd64 1:7.10.1+dfsg-1 [41.0 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libltdl7 amd64 2.5.4-4 [416 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 libglpk40 amd64 5.0-1+b2 [401 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 libpython3.13 amd64 3.13.2-2 [2155 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB]
Get:32 http://deb.debian.org/debian sid/main amd64 python-cobra-data all 0.29.1-1 [1437 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 python3-annotated-types all 0.7.0-1 [18.8 kB]
Get:35 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 python3-sniffio all 1.3.1-1 [7120 B]
Get:37 http://deb.debian.org/debian sid/main amd64 python3-anyio all 4.8.0-3 [63.6 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get:39 http://deb.debian.org/debian sid/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [95.4 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 python3-depinfo amd64 2.2.0-3 [11.6 kB]
Get:42 http://deb.debian.org/debian sid/main amd64 python3-diskcache all 5.6.3-1 [34.4 kB]
Get:43 http://deb.debian.org/debian sid/main amd64 python3-dnspython all 2.7.0-1 [164 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 python3-email-validator all 2.2.0-1 [31.6 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 python3-h11 all 0.14.0-1 [50.1 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 python3-httpcore all 1.0.7-1 [44.7 kB]
Get:47 http://deb.debian.org/debian sid/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get:48 http://deb.debian.org/debian sid/main amd64 python3-mdurl all 0.1.2-1 [9444 B]
Get:49 http://deb.debian.org/debian sid/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 python3-rich all 13.9.4-1 [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-importlib-resources all 6.5.2-1 [24.2 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 python3-swiglpk amd64 5.0.10-2+b2 [64.8 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-5 [4148 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 python3-optlang all 1.8.2-3 [5376 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 python3-pytz all 2025.1-3 [150 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 python3-tz all 2025.1-3 [4004 B]
Get:59 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8+b1 [4517 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 python3-pydantic-core amd64 2.27.2-1+b2 [1502 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 python3-pydantic amd64 2.10.6-1 [346 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml.clib amd64 0.2.12+ds-1+b1 [135 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 python3-sbml5 amd64 5.20.4+dfsg-0.1 [3428 kB]
Get:67 http://deb.debian.org/debian sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB]
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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'
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Unpacking python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ...
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Unpacking python3-ruamel.yaml (0.18.10+ds-1) ...
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Unpacking python3-tabulate (0.9.0-1) ...
Selecting previously unselected package piuparts-depends-dummy.
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Unpacking piuparts-depends-dummy (0.invalid.0) ...
Setting up media-types (13.0.0) ...
Setting up libsqlite3-0:amd64 (3.46.1-2) ...
Setting up libgomp1:amd64 (14.2.0-19) ...
Setting up libblas3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ...
Setting up libltdl7:amd64 (2.5.4-4) ...
Setting up libgfortran5:amd64 (14.2.0-19) ...
Setting up libffi8:amd64 (3.4.7-1) ...
Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ...
Setting up netbase (6.5) ...
Setting up libicu76:amd64 (76.1-3) ...
Setting up openssl (3.4.1-1) ...
Setting up python-cobra-data (0.29.1-1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.3+b1) ...
Setting up liblapack3:amd64 (3.12.1-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libamd3:amd64 (1:7.10.1+dfsg-1) ...
Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ...
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libglpk40:amd64 (5.0-1+b2) ...
Setting up libreadline8t64:amd64 (8.2-6) ...
Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ...
Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
Setting up libpython3.13:amd64 (3.13.2-2) ...
Setting up python3.13 (3.13.2-2) ...
Setting up python3 (3.13.2-2) ...
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-sbml5 (5.20.4+dfsg-0.1) ...
Setting up python3-platformdirs (4.3.6-1) ...
Setting up python3-pygments (2.18.0+dfsg-2) ...
Setting up python3-certifi (2025.1.31+ds-1) ...
Setting up python3-mdurl (0.1.2-1) ...
Setting up python3-idna (3.10-1) ...
Setting up python3-h11 (0.14.0-1) ...
Setting up python3-depinfo (2.2.0-3) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-numpy (1:2.2.3+ds-5) ...
Setting up python3-markdown-it (3.0.0-2) ...
Setting up python3-dnspython (2.7.0-1) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up python3-email-validator (2.2.0-1) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up python3-diskcache (5.6.3-1) ...
Setting up python3-swiglpk (5.0.10-2+b2) ...
Setting up python3-httpcore (1.0.7-1) ...
Setting up python3-sniffio (1.3.1-1) ...
Setting up python3-sympy (1.13.3-5) ...
Setting up python3-pydantic-core (2.27.2-1+b2) ...
Setting up python3-anyio (4.8.0-3) ...
Setting up python3-importlib-resources (6.5.2-1) ...
Setting up python3-rich (13.9.4-1) ...
Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8+b1) ...
Setting up python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ...
Setting up python3-tabulate (0.9.0-1) ...
Setting up python3-pytz (2025.1-3) ...
Setting up python3-tz (2025.1-3) ...
Setting up python3-pandas (2.2.3+dfsg-8) ...
Setting up python3-httpx (0.28.1-1) ...
Setting up python3-pydantic (2.10.6-1) ...
Setting up python3-ruamel.yaml (0.18.10+ds-1) ...
Setting up python3-optlang (1.8.2-3) ...
/usr/lib/python3/dist-packages/optlang/matrix_interface.py:66: SyntaxWarning: invalid escape sequence '\m'
\text{minimize }& \frac{1}{2}x^T\mathbf{P}x + q^Tx \\
/usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:34: SyntaxWarning: invalid escape sequence '\*'
OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+')
/usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s'
self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300')
Setting up piuparts-depends-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.41-6) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb']
0m37.0s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok
0m37.0s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpxaao9g9n/./tmp/piuparts-depends-dummy.deb
0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy']
0m37.0s DUMP:
piuparts-depends-dummy install ok installed
0m37.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy']
0m37.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m37.1s DUMP:
(Reading database ... 13538 files and directories currently installed.)
Removing piuparts-depends-dummy (0.invalid.0) ...
0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m37.1s DEBUG: Recording chroot state
0m37.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m38.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m40.3s DEBUG: No broken symlinks as far as we can find.
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m41.2s 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:
0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m41.2s DUMP:
python3-cobra:
Installed: (none)
Candidate: 0.29.1-1
Version table:
0.29.1-1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-1']
0m42.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
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 1119 kB of archives.
After this operation, 1922 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 python3-cobra amd64 0.29.1-1 [1119 kB]
Fetched 1119 kB in 0s (15.3 MB/s)
Selecting previously unselected package python3-cobra.
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(Reading database ... 13538 files and directories currently installed.)
Preparing to unpack .../python3-cobra_0.29.1-1_amd64.deb ...
Unpacking python3-cobra (0.29.1-1) ...
Setting up python3-cobra (0.29.1-1) ...
0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-1']
0m42.4s INFO: Running scripts post_install
0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'systemd-tmpfiles', '--cat-config']
0m42.5s DUMP:
chroot: failed to run command 'systemd-tmpfiles': No such file or directory
0m42.5s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'systemd-tmpfiles', '--cat-config']
0m42.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'remove', 'python3-cobra']
0m43.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5 libglpk40
libgomp1 libicu76 liblapack3 libltdl7 libpython3-stdlib libpython3.13
libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsqlite3-0
libsuitesparseconfig7 libxml2 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-importlib-resources python3-markdown-it python3-mdurl
python3-minimal python3-mpmath python3-numpy python3-numpy-dev
python3-optlang python3-pandas python3-pandas-lib python3-platformdirs
python3-pydantic python3-pydantic-core python3-pygments python3-pytz
python3-rich python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5
python3-sniffio python3-swiglpk python3-sympy python3-tabulate
python3-typing-extensions python3-tz 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, 1922 kB disk space will be freed.
(Reading database ...
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13637 files and directories currently installed.)
Removing python3-cobra (0.29.1-1) ...
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'remove', 'python3-cobra']
0m43.4s INFO: Reinstalling after remove
0m43.4s INFO: Running scripts pre_install
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m43.5s 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:
0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m43.5s DUMP:
python3-cobra:
Installed: (none)
Candidate: 0.29.1-1
Version table:
0.29.1-1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
0m43.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m43.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-1']
0m44.6s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
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/1119 kB of archives.
After this operation, 1922 kB of additional disk space will be used.
Selecting previously unselected package python3-cobra.
(Reading database ...
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(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13538 files and directories currently installed.)
Preparing to unpack .../python3-cobra_0.29.1-1_amd64.deb ...
Unpacking python3-cobra (0.29.1-1) ...
Setting up python3-cobra (0.29.1-1) ...
0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', 'python3-cobra=0.29.1-1']
0m44.6s INFO: Running scripts post_install
0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m44.6s INFO: Running scripts pre_install
0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_database-server']
0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_exceptions']
0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_extras']
0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture']
0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m44.7s 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:
0m44.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy']
0m44.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m44.8s DUMP:
python3-cobra:
Installed: 0.29.1-1
Candidate: 0.29.1-1
Version table:
*** 0.29.1-1 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-cache', 'policy', 'python3-cobra']
0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', '--reinstall', 'python3-cobra=0.29.1-1']
0m45.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded.
Need to get 0 B/1119 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 ... 13637 files and directories currently installed.)
Preparing to unpack .../python3-cobra_0.29.1-1_amd64.deb ...
Unpacking python3-cobra (0.29.1-1) over (0.29.1-1) ...
Setting up python3-cobra (0.29.1-1) ...
0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', '-y', 'install', '--reinstall', 'python3-cobra=0.29.1-1']
0m45.9s INFO: Running scripts post_install
0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_install_exceptions']
0m45.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m46.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m48.5s DEBUG: No broken symlinks as far as we can find.
0m49.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', '-ac', '--ignore-obsolete']
0m50.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', '-ac', '--ignore-obsolete']
0m50.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m50.7s DUMP:
0.15.6
0m50.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m50.7s INFO: Running adequate version 0.15.6 now.
0m50.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'python3-cobra']
0m50.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'python3-cobra']
0m50.9s INFO: Running scripts pre_remove
0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m51.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m51.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_exceptions']
0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_exceptions']
0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_preseed_cleanup']
0m51.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/pre_remove_preseed_cleanup']
0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m51.9s DUMP:
install ok installed apt apt 2.9.33
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1+b1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed ca-certificates ca-certificates 20241223
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed dbconfig-common dbconfig-common 2.0.24
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.18
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libamd3:amd64 libamd3 1:7.10.1+dfsg-1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.33
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblas3:amd64 libblas3 3.12.1-2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-2
install ok installed libcolamd3:amd64 libcolamd3 1:7.10.1+dfsg-1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libexpat1:amd64 libexpat1 2.7.0-1
install ok installed libffi8:amd64 libffi8 3.4.7-1
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19
install ok installed libglpk40:amd64 libglpk40 5.0-1+b2
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libgomp1:amd64 libgomp1 14.2.0-19
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed libicu76:amd64 libicu76 76.1-3
install ok installed liblapack3:amd64 liblapack3 3.12.1-2
install ok installed libltdl7:amd64 libltdl7 2.5.4-4
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7
install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.13.2-2
install ok installed libpython3.13:amd64 libpython3.13 3.13.2-2
install ok installed libpython3.13-minimal:amd64 libpython3.13-minimal 3.13.2-2
install ok installed libpython3.13-stdlib:amd64 libpython3.13-stdlib 3.13.2-2
install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsuitesparseconfig7:amd64 libsuitesparseconfig7 1:7.10.1+dfsg-1
install ok installed libsystemd0:amd64 libsystemd0 257.4-3
install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4
install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.4-3
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.3+b1
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-2
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed media-types media-types 13.0.0
install ok installed mount mount 2.40.4-5
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed netbase netbase 6.5
install ok installed openssl openssl 3.4.1-1
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-2
install ok installed perl-base perl-base 5.40.1-2
install ok installed procps procps 2:4.0.4-7
install ok installed python-cobra-data python-cobra-data 0.29.1-1
install ok installed python3 python3 3.13.2-2
install ok installed python3-annotated-types python3-annotated-types 0.7.0-1
install ok installed python3-anyio python3-anyio 4.8.0-3
install ok installed python3-certifi python3-certifi 2025.1.31+ds-1
install ok installed python3-click python3-click 8.2.0+0.really.8.1.8-1
install ok installed python3-cobra python3-cobra 0.29.1-1
install ok installed python3-dateutil python3-dateutil 2.9.0-3
install ok installed python3-depinfo python3-depinfo 2.2.0-3
install ok installed python3-diskcache python3-diskcache 5.6.3-1
install ok installed python3-dnspython python3-dnspython 2.7.0-1
install ok installed python3-email-validator python3-email-validator 2.2.0-1
install ok installed python3-h11 python3-h11 0.14.0-1
install ok installed python3-httpcore python3-httpcore 1.0.7-1
install ok installed python3-httpx python3-httpx 0.28.1-1
install ok installed python3-idna python3-idna 3.10-1
install ok installed python3-importlib-resources python3-importlib-resources 6.5.2-1
install ok installed python3-markdown-it python3-markdown-it 3.0.0-2
install ok installed python3-mdurl python3-mdurl 0.1.2-1
install ok installed python3-minimal python3-minimal 3.13.2-2
install ok installed python3-mpmath python3-mpmath 1.3.0-1
install ok installed python3-numpy python3-numpy 1:2.2.3+ds-5
install ok installed python3-numpy-dev:amd64 python3-numpy-dev 1:2.2.3+ds-5
install ok installed python3-optlang python3-optlang 1.8.2-3
install ok installed python3-pandas python3-pandas 2.2.3+dfsg-8
install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.2.3+dfsg-8+b1
install ok installed python3-platformdirs python3-platformdirs 4.3.6-1
install ok installed python3-pydantic python3-pydantic 2.10.6-1
install ok installed python3-pydantic-core python3-pydantic-core 2.27.2-1+b2
install ok installed python3-pygments python3-pygments 2.18.0+dfsg-2
install ok installed python3-pytz python3-pytz 2025.1-3
install ok installed python3-rich python3-rich 13.9.4-1
install ok installed python3-ruamel.yaml python3-ruamel.yaml 0.18.10+ds-1
install ok installed python3-ruamel.yaml.clib python3-ruamel.yaml.clib 0.2.12+ds-1+b1
install ok installed python3-sbml5 python3-sbml5 5.20.4+dfsg-0.1
install ok installed python3-sniffio python3-sniffio 1.3.1-1
install ok installed python3-swiglpk python3-swiglpk 5.0.10-2+b2
install ok installed python3-sympy python3-sympy 1.13.3-5
install ok installed python3-tabulate python3-tabulate 0.9.0-1
install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2
install ok installed python3-tz python3-tz 2025.1-3
install ok installed python3.13 python3.13 3.13.2-2
install ok installed python3.13-minimal python3.13-minimal 3.13.2-2
install ok installed readline-common readline-common 8.2-6
install ok installed sed sed 4.9-2
install ok installed sensible-utils sensible-utils 0.0.24
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed ucf ucf 3.0050
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m51.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libicu76: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: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-importlib-resources', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-tz', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra']
0m56.2s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
ca-certificates libamd3 libblas3 libcolamd3 libexpat1 libffi8 libgfortran5
libglpk40 libgomp1 libicu76 liblapack3 libltdl7 libpython3-stdlib
libpython3.13 libpython3.13-minimal libpython3.13-stdlib libreadline8t64
libsqlite3-0 libsuitesparseconfig7 libxml2 media-types netbase openssl
python-cobra-data python3 python3-annotated-types python3-anyio
python3-certifi python3-click python3-cobra python3-dateutil python3-depinfo
python3-diskcache python3-dnspython python3-email-validator python3-h11
python3-httpcore python3-httpx python3-idna python3-importlib-resources
python3-markdown-it python3-mdurl python3-minimal python3-mpmath
python3-numpy python3-numpy-dev python3-optlang python3-pandas
python3-pandas-lib python3-platformdirs python3-pydantic
python3-pydantic-core python3-pygments python3-pytz python3-rich
python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-sniffio
python3-swiglpk python3-sympy python3-tabulate python3-typing-extensions
python3-tz python3.13 python3.13-minimal readline-common
0 upgraded, 0 newly installed, 67 to remove and 0 not upgraded.
After this operation, 275 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 ... 13637 files and directories currently installed.)
Removing python3-cobra (0.29.1-1) ...
Removing python3-httpx (0.28.1-1) ...
Removing python3-httpcore (1.0.7-1) ...
Removing python3-certifi (2025.1.31+ds-1) ...
Removing ca-certificates (20241223) ...
Removing dangling symlinks from /etc/ssl/certs... done.
Removing python3-optlang (1.8.2-3) ...
Removing python3-swiglpk (5.0.10-2+b2) ...
Removing libglpk40:amd64 (5.0-1+b2) ...
Removing libamd3:amd64 (1:7.10.1+dfsg-1) ...
Removing python3-pandas (2.2.3+dfsg-8) ...
Removing python3-pandas-lib:amd64 (2.2.3+dfsg-8+b1) ...
Removing python3-numpy (1:2.2.3+ds-5) ...
Removing liblapack3:amd64 (3.12.1-2) ...
Removing libblas3:amd64 (3.12.1-2) ...
Removing libcolamd3:amd64 (1:7.10.1+dfsg-1) ...
Removing python3-ruamel.yaml (0.18.10+ds-1) ...
Removing python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ...
Removing python3-sympy (1.13.3-5) ...
Removing python3-rich (13.9.4-1) ...
Removing python3-h11 (0.14.0-1) ...
Removing python3-tz (2025.1-3) ...
Removing python3-pytz (2025.1-3) ...
Removing python3-anyio (4.8.0-3) ...
Removing python3-sbml5 (5.20.4+dfsg-0.1) ...
Removing libpython3.13:amd64 (3.13.2-2) ...
Removing libgfortran5:amd64 (14.2.0-19) ...
Removing libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ...
Removing libgomp1:amd64 (14.2.0-19) ...
Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.3+b1) ...
Removing libicu76:amd64 (76.1-3) ...
Removing libltdl7:amd64 (2.5.4-4) ...
Removing python3-pydantic (2.10.6-1) ...
Removing python3-email-validator (2.2.0-1) ...
Removing python3-dnspython (2.7.0-1) ...
Removing openssl (3.4.1-1) ...
Removing python-cobra-data (0.29.1-1) ...
Removing python3-annotated-types (0.7.0-1) ...
Removing python3-click (8.2.0+0.really.8.1.8-1) ...
Removing python3-dateutil (2.9.0-3) ...
Removing python3-depinfo (2.2.0-3) ...
Removing python3-diskcache (5.6.3-1) ...
Removing python3-idna (3.10-1) ...
Removing python3-importlib-resources (6.5.2-1) ...
Removing python3-markdown-it (3.0.0-2) ...
Removing python3-mdurl (0.1.2-1) ...
Removing python3-mpmath (1.3.0-1) ...
Removing python3-numpy-dev:amd64 (1:2.2.3+ds-5) ...
Removing python3-platformdirs (4.3.6-1) ...
Removing python3-pydantic-core (2.27.2-1+b2) ...
Removing python3-pygments (2.18.0+dfsg-2) ...
Removing python3-sniffio (1.3.1-1) ...
Removing python3-tabulate (0.9.0-1) ...
Removing python3-typing-extensions (4.12.2-2) ...
Removing python3 (3.13.2-2) ...
Removing python3-minimal (3.13.2-2) ...
Removing python3.13 (3.13.2-2) ...
Removing python3.13-minimal (3.13.2-2) ...
Removing libexpat1:amd64 (2.7.0-1) ...
Removing libpython3-stdlib:amd64 (3.13.2-2) ...
Removing libpython3.13-stdlib:amd64 (3.13.2-2) ...
find: '/usr/lib/python3': No such file or directory
Removing libffi8:amd64 (3.4.7-1) ...
Removing libpython3.13-minimal:amd64 (3.13.2-2) ...
find: '/usr/lib/python3': No such file or directory
Removing libreadline8t64:amd64 (8.2-6) ...
Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Removing libsqlite3-0:amd64 (3.46.1-2) ...
Removing media-types (13.0.0) ...
Removing netbase (6.5) ...
Removing readline-common (8.2-6) ...
Processing triggers for libc-bin (2.41-6) ...
0m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libicu76: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: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-importlib-resources', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-tz', 'python3.13', 'python3.13-minimal', 'readline-common', 'python3-cobra']
0m56.2s INFO: Running scripts post_remove
0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_remove_cleanup']
0m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_remove_cleanup']
0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_remove_exceptions']
0m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_remove_exceptions']
0m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libicu76: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: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-importlib-resources', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-tz', 'python3.13', 'python3.13-minimal', 'readline-common']
0m56.4s DUMP:
(Reading database ... 5465 files and directories currently installed.)
Purging configuration files for ca-certificates (20241223) ...
Removing dangling symlinks from /etc/ssl/certs... done.
dpkg: warning: ignoring request to remove libamd3 which isn't installed
dpkg: warning: ignoring request to remove libblas3 which isn't installed
dpkg: warning: ignoring request to remove libcolamd3 which isn't installed
dpkg: warning: ignoring request to remove libexpat1 which isn't installed
dpkg: warning: ignoring request to remove libffi8 which isn't installed
dpkg: warning: ignoring request to remove libgfortran5 which isn't installed
dpkg: warning: ignoring request to remove libglpk40 which isn't installed
dpkg: warning: ignoring request to remove libgomp1 which isn't installed
dpkg: warning: ignoring request to remove libicu76 which isn't installed
dpkg: warning: ignoring request to remove liblapack3 which isn't installed
dpkg: warning: ignoring request to remove libltdl7 which isn't installed
dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed
dpkg: warning: ignoring request to remove libpython3.13 which isn't installed
Purging configuration files for libpython3.13-minimal:amd64 (3.13.2-2) ...
dpkg: warning: ignoring request to remove libpython3.13-stdlib which isn't installed
Purging configuration files for libreadline8t64:amd64 (8.2-6) ...
dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed
dpkg: warning: ignoring request to remove libsuitesparseconfig7 which isn't installed
dpkg: warning: ignoring request to remove libxml2 which isn't installed
Purging configuration files for media-types (13.0.0) ...
Purging configuration files for netbase (6.5) ...
Purging configuration files for openssl (3.4.1-1) ...
dpkg: warning: ignoring request to remove python-cobra-data which isn't installed
Purging configuration files for python3 (3.13.2-2) ...
dpkg: warning: ignoring request to remove python3-annotated-types which isn't installed
dpkg: warning: ignoring request to remove python3-anyio which isn't installed
dpkg: warning: ignoring request to remove python3-certifi which isn't installed
dpkg: warning: ignoring request to remove python3-click which isn't installed
dpkg: warning: ignoring request to remove python3-dateutil which isn't installed
dpkg: warning: ignoring request to remove python3-depinfo which isn't installed
dpkg: warning: ignoring request to remove python3-diskcache which isn't installed
dpkg: warning: ignoring request to remove python3-dnspython which isn't installed
dpkg: warning: ignoring request to remove python3-email-validator which isn't installed
dpkg: warning: ignoring request to remove python3-h11 which isn't installed
dpkg: warning: ignoring request to remove python3-httpcore which isn't installed
dpkg: warning: ignoring request to remove python3-httpx which isn't installed
dpkg: warning: ignoring request to remove python3-idna which isn't installed
dpkg: warning: ignoring request to remove python3-importlib-resources which isn't installed
dpkg: warning: ignoring request to remove python3-markdown-it which isn't installed
dpkg: warning: ignoring request to remove python3-mdurl which isn't installed
dpkg: warning: ignoring request to remove python3-minimal which isn't installed
dpkg: warning: ignoring request to remove python3-mpmath which isn't installed
Purging configuration files for python3-numpy (1:2.2.3+ds-5) ...
dpkg: warning: ignoring request to remove python3-numpy-dev which isn't installed
dpkg: warning: ignoring request to remove python3-optlang which isn't installed
dpkg: warning: ignoring request to remove python3-pandas which isn't installed
dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed
dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed
dpkg: warning: ignoring request to remove python3-pydantic which isn't installed
dpkg: warning: ignoring request to remove python3-pydantic-core which isn't installed
dpkg: warning: ignoring request to remove python3-pygments which isn't installed
dpkg: warning: ignoring request to remove python3-pytz which isn't installed
dpkg: warning: ignoring request to remove python3-rich which isn't installed
dpkg: warning: ignoring request to remove python3-ruamel.yaml which isn't installed
dpkg: warning: ignoring request to remove python3-ruamel.yaml.clib which isn't installed
dpkg: warning: ignoring request to remove python3-sbml5 which isn't installed
dpkg: warning: ignoring request to remove python3-sniffio which isn't installed
dpkg: warning: ignoring request to remove python3-swiglpk which isn't installed
Purging configuration files for python3-sympy (1.13.3-5) ...
dpkg: warning: ignoring request to remove python3-tabulate which isn't installed
dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed
dpkg: warning: ignoring request to remove python3-tz which isn't installed
dpkg: warning: ignoring request to remove python3.13 which isn't installed
Purging configuration files for python3.13-minimal (3.13.2-2) ...
Purging configuration files for readline-common (8.2-6) ...
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'ca-certificates', 'libamd3:amd64', 'libblas3:amd64', 'libcolamd3:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libgfortran5:amd64', 'libglpk40:amd64', 'libgomp1:amd64', 'libicu76: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: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-importlib-resources', 'python3-markdown-it', 'python3-mdurl', 'python3-minimal', 'python3-mpmath', 'python3-numpy', 'python3-numpy-dev:amd64', 'python3-optlang', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-platformdirs', 'python3-pydantic', 'python3-pydantic-core', 'python3-pygments', 'python3-pytz', 'python3-rich', 'python3-ruamel.yaml', 'python3-ruamel.yaml.clib', 'python3-sbml5', 'python3-sniffio', 'python3-swiglpk', 'python3-sympy', 'python3-tabulate', 'python3-typing-extensions', 'python3-tz', 'python3.13', 'python3.13-minimal', 'readline-common']
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'python3-cobra']
0m56.4s DUMP:
dpkg: warning: ignoring request to remove python3-cobra which isn't installed
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', 'python3-cobra']
0m56.4s INFO: Running scripts post_purge
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_purge_exceptions']
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_purge_exceptions']
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_purge_manual_cleanup']
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_purge_manual_cleanup']
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', '--pending']
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--purge', '--pending']
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--remove', '--pending']
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg', '--remove', '--pending']
0m56.4s INFO: Running scripts post_test
0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_test_exceptions']
0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'tmp/scripts/post_test_exceptions']
0m56.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m56.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m57.2s DEBUG: No broken symlinks as far as we can find.
0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-divert', '--list']
0m57.2s DUMP:
local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged
local diversion of /home to /home.distrib
diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'dpkg-divert', '--list']
0m57.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m57.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n', 'apt-get', 'clean']
0m57.2s DEBUG: Recording chroot state
0m58.8s INFO: PASS: Installation and purging test.
0m59.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/shm']
0m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/shm']
0m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/console']
0m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/console']
0m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/ptmx']
0m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/ptmx']
0m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/pts']
0m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/dev/pts']
0m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/proc']
0m59.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n/proc']
0m59.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m59.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpxaao9g9n']
0m59.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpxaao9g9n
0m59.4s INFO: PASS: All tests.
0m59.4s INFO: piuparts run ends.
ret=0
End: 2025-03-17 14:14:58 GMT