0s autopkgtest [10:43:23]: starting date and time: 2024-03-26 10:43:23+0000 0s autopkgtest [10:43:23]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [10:43:23]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bnsdil6r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-cobra/0.29.0-1ubuntu1 libsbml/5.20.2+dfsg-2.1build3 python3-defaults/3.12.2-0ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-ppc64el-25.secgroup --name adt-noble-ppc64el-python-cobra-20240326-104323-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 114s autopkgtest [10:45:17]: testbed dpkg architecture: ppc64el 115s autopkgtest [10:45:18]: testbed apt version: 2.7.12 115s autopkgtest [10:45:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 115s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 116s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 116s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3982 kB] 116s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 116s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [8504 B] 116s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [697 kB] 116s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 116s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 116s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 116s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4220 kB] 117s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 117s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.7 kB] 117s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 120s Fetched 9651 kB in 2s (3919 kB/s) 120s Reading package lists... 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 246 not upgraded. 123s sh: Attempting to set up Debian/Ubuntu apt sources automatically 123s sh: Distribution appears to be Ubuntu 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s eatmydata is already the newest version (131-1). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s dbus is already the newest version (1.14.10-4ubuntu1). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s rng-tools-debian is already the newest version (2.4). 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s The following packages will be REMOVED: 125s cloud-init* python3-configobj* python3-debconf* 126s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 126s After this operation, 3256 kB disk space will be freed. 126s (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 ... 70156 files and directories currently installed.) 126s Removing cloud-init (24.1.2-0ubuntu1) ... 126s Removing python3-configobj (5.0.8-3) ... 126s Removing python3-debconf (1.5.86) ... 126s Processing triggers for man-db (2.12.0-3) ... 127s (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 ... 69767 files and directories currently installed.) 127s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 127s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 127s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 127s invoke-rc.d: policy-rc.d denied execution of try-restart. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s linux-generic is already the newest version (6.8.0-11.11+1). 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 128s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 129s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 131s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [10:45:35]: rebooting testbed after setup commands that affected boot 298s autopkgtest [10:48:21]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 301s autopkgtest [10:48:24]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 304s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-cobra 0.29.0-1 (dsc) [3120 B] 304s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-cobra 0.29.0-1 (tar) [3650 kB] 304s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-cobra 0.29.0-1 (diff) [10.3 kB] 304s gpgv: Signature made Tue Dec 12 16:28:14 2023 UTC 304s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 304s gpgv: issuer "tille@debian.org" 304s gpgv: Can't check signature: No public key 304s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1.dsc: no acceptable signature found 304s autopkgtest [10:48:27]: testing package python-cobra version 0.29.0-1 304s autopkgtest [10:48:27]: build not needed 305s autopkgtest [10:48:28]: test run-unit-test: preparing testbed 306s Reading package lists... 306s Building dependency tree... 306s Reading state information... 307s Starting pkgProblemResolver with broken count: 0 307s Starting 2 pkgProblemResolver with broken count: 0 307s Done 307s The following additional packages will be installed: 307s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 307s liblapack3 liblbfgsb0 libltdl7 libpython3.12 libsuitesparseconfig7 307s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 307s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 307s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 307s python3-importlib-resources python3-iniconfig python3-more-itertools 307s python3-mpmath python3-numpy python3-optlang python3-packaging 307s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 307s python3-pytest python3-pytest-benchmark python3-pytest-mock 307s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 307s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 307s python3-tabulate python3-zipp quilt swig 307s Suggested packages: 307s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 307s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 307s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 307s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 307s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 307s swig-doc swig-examples 307s Recommended packages: 307s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 307s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 307s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 307s python3-pil isympy-common 307s The following NEW packages will be installed: 307s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 307s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12 307s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 307s python3-click python3-cobra python3-colorama python3-cpuinfo 307s python3-dateutil python3-decorator python3-depinfo python3-diskcache 307s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 307s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 307s python3-optlang python3-packaging python3-pandas python3-pandas-lib 307s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 307s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 307s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 307s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 307s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 307s Need to get 61.3 MB/61.3 MB of archives. 307s After this operation, 343 MB of additional disk space will be used. 307s Get:1 /tmp/autopkgtest.ssAppb/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [768 B] 307s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el diffstat ppc64el 1.66-1 [32.9 kB] 307s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 307s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] 308s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libsuitesparseconfig7 ppc64el 1:7.6.1+dfsg-1 [12.8 kB] 308s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd3 ppc64el 1:7.6.1+dfsg-1 [36.6 kB] 308s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 308s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libcolamd3 ppc64el 1:7.6.1+dfsg-1 [21.6 kB] 308s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 308s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libltdl7 ppc64el 2.4.7-7 [48.0 kB] 308s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libglpk40 ppc64el 5.0-1build1 [459 kB] 308s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 308s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 308s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libpython3.12 ppc64el 3.12.2-1 [2575 kB] 308s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-cobra-data all 0.29.0-1 [1648 kB] 308s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-sniffio all 1.3.0-2 [7216 B] 308s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-anyio all 3.7.0-1 [56.1 kB] 308s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 308s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 308s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-click all 8.1.6-1 [79.0 kB] 308s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-depinfo ppc64el 2.2.0-2 [10.9 kB] 308s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-diskcache all 5.4.0-3 [34.6 kB] 308s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h11 all 0.14.0-1 [51.1 kB] 308s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-httpcore all 1.0.2-2 [38.3 kB] 308s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-httpx all 0.26.0-2 [61.3 kB] 308s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-more-itertools all 10.2.0-1 [52.9 kB] 308s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-zipp all 1.0.0-6 [6090 B] 308s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-importlib-resources all 6.0.1-1 [22.1 kB] 308s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 309s Get:30 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-swiglpk ppc64el 5.0.10-1 [123 kB] 309s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-mpmath all 1.2.1-3 [421 kB] 309s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-sympy all 1.12-7 [3966 kB] 309s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-optlang all 1.8.1-1 [82.7 kB] 309s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 309s Get:35 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 309s Get:36 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 309s Get:37 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pydantic all 1.10.13-0ubuntu1 [150 kB] 309s Get:38 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-ruamel.yaml.clib ppc64el 0.2.8-1 [235 kB] 309s Get:39 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 309s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-simplejson ppc64el 3.19.2-1build1 [70.4 kB] 309s Get:41 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tabulate all 0.8.10-1 [38.2 kB] 309s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el swig ppc64el 4.2.0-2ubuntu1 [1261 kB] 310s Get:43 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-sbml5 ppc64el 5.20.2+dfsg-2build2 [3756 kB] 310s Get:44 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cobra ppc64el 0.29.0-1 [1119 kB] 310s Get:45 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cpuinfo all 9.0.0-1 [21.2 kB] 310s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 310s Get:47 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 310s Get:48 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 310s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB] 310s Get:50 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 310s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 310s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 310s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el quilt all 0.67+really0.67-4 [436 kB] 310s Get:54 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 311s Fetched 61.3 MB in 3s (17.8 MB/s) 311s Selecting previously unselected package diffstat. 311s (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 ... 69712 files and directories currently installed.) 311s Preparing to unpack .../00-diffstat_1.66-1_ppc64el.deb ... 311s Unpacking diffstat (1.66-1) ... 311s Selecting previously unselected package libgomp1:ppc64el. 311s Preparing to unpack .../01-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 311s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 311s Selecting previously unselected package gettext. 311s Preparing to unpack .../02-gettext_0.21-14ubuntu1_ppc64el.deb ... 311s Unpacking gettext (0.21-14ubuntu1) ... 311s Selecting previously unselected package libsuitesparseconfig7:ppc64el. 311s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1_ppc64el.deb ... 311s Unpacking libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1) ... 311s Selecting previously unselected package libamd3:ppc64el. 311s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1_ppc64el.deb ... 311s Unpacking libamd3:ppc64el (1:7.6.1+dfsg-1) ... 311s Selecting previously unselected package libblas3:ppc64el. 311s Preparing to unpack .../05-libblas3_3.12.0-3_ppc64el.deb ... 311s Unpacking libblas3:ppc64el (3.12.0-3) ... 311s Selecting previously unselected package libcolamd3:ppc64el. 311s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1_ppc64el.deb ... 311s Unpacking libcolamd3:ppc64el (1:7.6.1+dfsg-1) ... 311s Selecting previously unselected package libgfortran5:ppc64el. 311s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 311s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 311s Selecting previously unselected package libltdl7:ppc64el. 311s Preparing to unpack .../08-libltdl7_2.4.7-7_ppc64el.deb ... 311s Unpacking libltdl7:ppc64el (2.4.7-7) ... 311s Selecting previously unselected package libglpk40:ppc64el. 311s Preparing to unpack .../09-libglpk40_5.0-1build1_ppc64el.deb ... 311s Unpacking libglpk40:ppc64el (5.0-1build1) ... 311s Selecting previously unselected package liblapack3:ppc64el. 311s Preparing to unpack .../10-liblapack3_3.12.0-3_ppc64el.deb ... 311s Unpacking liblapack3:ppc64el (3.12.0-3) ... 311s Selecting previously unselected package liblbfgsb0:ppc64el. 311s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 311s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 311s Selecting previously unselected package libpython3.12:ppc64el. 311s Preparing to unpack .../12-libpython3.12_3.12.2-1_ppc64el.deb ... 311s Unpacking libpython3.12:ppc64el (3.12.2-1) ... 311s Selecting previously unselected package python-cobra-data. 311s Preparing to unpack .../13-python-cobra-data_0.29.0-1_all.deb ... 311s Unpacking python-cobra-data (0.29.0-1) ... 311s Selecting previously unselected package python3-sniffio. 311s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 311s Unpacking python3-sniffio (1.3.0-2) ... 311s Selecting previously unselected package python3-anyio. 311s Preparing to unpack .../15-python3-anyio_3.7.0-1_all.deb ... 311s Unpacking python3-anyio (3.7.0-1) ... 311s Selecting previously unselected package python3-appdirs. 311s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 311s Unpacking python3-appdirs (1.4.4-4) ... 311s Selecting previously unselected package python3-colorama. 311s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 311s Unpacking python3-colorama (0.4.6-4) ... 311s Selecting previously unselected package python3-click. 311s Preparing to unpack .../18-python3-click_8.1.6-1_all.deb ... 311s Unpacking python3-click (8.1.6-1) ... 311s Selecting previously unselected package python3-depinfo. 311s Preparing to unpack .../19-python3-depinfo_2.2.0-2_ppc64el.deb ... 311s Unpacking python3-depinfo (2.2.0-2) ... 311s Selecting previously unselected package python3-diskcache. 311s Preparing to unpack .../20-python3-diskcache_5.4.0-3_all.deb ... 311s Unpacking python3-diskcache (5.4.0-3) ... 311s Selecting previously unselected package python3-h11. 311s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 311s Unpacking python3-h11 (0.14.0-1) ... 312s Selecting previously unselected package python3-httpcore. 312s Preparing to unpack .../22-python3-httpcore_1.0.2-2_all.deb ... 312s Unpacking python3-httpcore (1.0.2-2) ... 312s Selecting previously unselected package python3-httpx. 312s Preparing to unpack .../23-python3-httpx_0.26.0-2_all.deb ... 312s Unpacking python3-httpx (0.26.0-2) ... 312s Selecting previously unselected package python3-more-itertools. 312s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 312s Unpacking python3-more-itertools (10.2.0-1) ... 312s Selecting previously unselected package python3-zipp. 312s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 312s Unpacking python3-zipp (1.0.0-6) ... 312s Selecting previously unselected package python3-importlib-resources. 312s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 312s Unpacking python3-importlib-resources (6.0.1-1) ... 312s Selecting previously unselected package python3-numpy. 312s Preparing to unpack .../27-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 312s Unpacking python3-numpy (1:1.24.2-2) ... 312s Selecting previously unselected package python3-swiglpk. 312s Preparing to unpack .../28-python3-swiglpk_5.0.10-1_ppc64el.deb ... 312s Unpacking python3-swiglpk (5.0.10-1) ... 312s Selecting previously unselected package python3-mpmath. 312s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 312s Unpacking python3-mpmath (1.2.1-3) ... 312s Selecting previously unselected package python3-sympy. 312s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 312s Unpacking python3-sympy (1.12-7) ... 312s Selecting previously unselected package python3-optlang. 312s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 312s Unpacking python3-optlang (1.8.1-1) ... 312s Selecting previously unselected package python3-dateutil. 312s Preparing to unpack .../32-python3-dateutil_2.8.2-3_all.deb ... 312s Unpacking python3-dateutil (2.8.2-3) ... 312s Selecting previously unselected package python3-pandas-lib:ppc64el. 312s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 312s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 313s Selecting previously unselected package python3-pandas. 313s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 313s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 313s Selecting previously unselected package python3-pydantic. 313s Preparing to unpack .../35-python3-pydantic_1.10.13-0ubuntu1_all.deb ... 313s Unpacking python3-pydantic (1.10.13-0ubuntu1) ... 313s Selecting previously unselected package python3-ruamel.yaml.clib:ppc64el. 313s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8-1_ppc64el.deb ... 313s Unpacking python3-ruamel.yaml.clib:ppc64el (0.2.8-1) ... 313s Selecting previously unselected package python3-ruamel.yaml. 313s Preparing to unpack .../37-python3-ruamel.yaml_0.17.21-1_all.deb ... 313s Unpacking python3-ruamel.yaml (0.17.21-1) ... 313s Selecting previously unselected package python3-simplejson. 313s Preparing to unpack .../38-python3-simplejson_3.19.2-1build1_ppc64el.deb ... 313s Unpacking python3-simplejson (3.19.2-1build1) ... 313s Selecting previously unselected package python3-tabulate. 313s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 313s Unpacking python3-tabulate (0.8.10-1) ... 313s Selecting previously unselected package swig. 313s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_ppc64el.deb ... 313s Unpacking swig (4.2.0-2ubuntu1) ... 314s Selecting previously unselected package python3-sbml5. 314s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-2build2_ppc64el.deb ... 314s Unpacking python3-sbml5 (5.20.2+dfsg-2build2) ... 314s Selecting previously unselected package python3-cobra. 314s Preparing to unpack .../42-python3-cobra_0.29.0-1_ppc64el.deb ... 314s Unpacking python3-cobra (0.29.0-1) ... 314s Selecting previously unselected package python3-cpuinfo. 314s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 314s Unpacking python3-cpuinfo (9.0.0-1) ... 314s Selecting previously unselected package python3-decorator. 314s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 314s Unpacking python3-decorator (5.1.1-5) ... 314s Selecting previously unselected package python3-iniconfig. 314s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 314s Unpacking python3-iniconfig (1.1.1-2) ... 314s Selecting previously unselected package python3-packaging. 314s Preparing to unpack .../46-python3-packaging_23.2-1_all.deb ... 314s Unpacking python3-packaging (23.2-1) ... 314s Selecting previously unselected package python3-pluggy. 314s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 314s Unpacking python3-pluggy (1.4.0-1) ... 314s Selecting previously unselected package python3-pytest. 314s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 314s Unpacking python3-pytest (7.4.4-1) ... 314s Selecting previously unselected package python3-pytest-benchmark. 314s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 314s Unpacking python3-pytest-benchmark (4.0.0-3) ... 314s Selecting previously unselected package python3-pytest-mock. 314s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 314s Unpacking python3-pytest-mock (3.12.0-1.1) ... 314s Selecting previously unselected package quilt. 314s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 314s Unpacking quilt (0.67+really0.67-4) ... 314s Selecting previously unselected package python3-scipy. 314s Preparing to unpack .../52-python3-scipy_1.11.4-6_ppc64el.deb ... 314s Unpacking python3-scipy (1.11.4-6) ... 315s Selecting previously unselected package autopkgtest-satdep. 315s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 315s Unpacking autopkgtest-satdep (0) ... 315s Setting up python3-more-itertools (10.2.0-1) ... 315s Setting up python3-iniconfig (1.1.1-2) ... 315s Setting up python3-sniffio (1.3.0-2) ... 315s Setting up swig (4.2.0-2ubuntu1) ... 315s Setting up python3-anyio (3.7.0-1) ... 316s Setting up python3-colorama (0.4.6-4) ... 316s Setting up python3-ruamel.yaml.clib:ppc64el (0.2.8-1) ... 316s Setting up python3-tabulate (0.8.10-1) ... 316s Setting up python3-zipp (1.0.0-6) ... 316s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 316s Setting up python3-click (8.1.6-1) ... 316s Setting up python3-simplejson (3.19.2-1build1) ... 316s Setting up python3-decorator (5.1.1-5) ... 316s Setting up libblas3:ppc64el (3.12.0-3) ... 316s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 316s Setting up python3-packaging (23.2-1) ... 317s Setting up python3-pydantic (1.10.13-0ubuntu1) ... 317s Setting up diffstat (1.66-1) ... 317s Setting up python3-h11 (0.14.0-1) ... 317s Setting up python3-depinfo (2.2.0-2) ... 317s Setting up python3-cpuinfo (9.0.0-1) ... 317s Setting up libltdl7:ppc64el (2.4.7-7) ... 317s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 317s Setting up python3-pluggy (1.4.0-1) ... 317s Setting up python3-ruamel.yaml (0.17.21-1) ... 318s Setting up libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1) ... 318s Setting up python3-dateutil (2.8.2-3) ... 318s Setting up python3-mpmath (1.2.1-3) ... 318s Setting up python3-diskcache (5.4.0-3) ... 319s Setting up python-cobra-data (0.29.0-1) ... 319s Setting up python3-appdirs (1.4.4-4) ... 319s Setting up libpython3.12:ppc64el (3.12.2-1) ... 319s Setting up python3-httpcore (1.0.2-2) ... 319s Setting up python3-sympy (1.12-7) ... 325s Setting up liblapack3:ppc64el (3.12.0-3) ... 325s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 325s Setting up gettext (0.21-14ubuntu1) ... 325s Setting up libamd3:ppc64el (1:7.6.1+dfsg-1) ... 325s Setting up python3-importlib-resources (6.0.1-1) ... 325s Setting up libcolamd3:ppc64el (1:7.6.1+dfsg-1) ... 325s Setting up python3-pytest (7.4.4-1) ... 326s Setting up quilt (0.67+really0.67-4) ... 326s Setting up python3-sbml5 (5.20.2+dfsg-2build2) ... 326s Setting up python3-httpx (0.26.0-2) ... 326s Setting up libglpk40:ppc64el (5.0-1build1) ... 326s Setting up python3-numpy (1:1.24.2-2) ... 328s Setting up python3-pytest-mock (3.12.0-1.1) ... 329s Setting up python3-swiglpk (5.0.10-1) ... 329s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 329s Setting up python3-optlang (1.8.1-1) ... 329s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 329s """A representation of the convex optimizatgion problem in standard form. 329s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 329s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 329s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 329s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 329s Setting up python3-pytest-benchmark (4.0.0-3) ... 329s Setting up python3-scipy (1.11.4-6) ... 332s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 332s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 338s Setting up python3-cobra (0.29.0-1) ... 338s Setting up autopkgtest-satdep (0) ... 338s Processing triggers for man-db (2.12.0-3) ... 338s Processing triggers for install-info (7.1-3) ... 338s Processing triggers for libc-bin (2.39-0ubuntu6) ... 342s (Reading database ... 77987 files and directories currently installed.) 342s Removing autopkgtest-satdep (0) ... 343s autopkgtest [10:49:06]: test run-unit-test: [----------------------- 343s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 343s Running Tests 343s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 347s ============================= test session starts ============================== 347s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 347s benchmark: 4.0.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000) 347s rootdir: /tmp/autopkgtest.ssAppb/autopkgtest_tmp 347s plugins: anyio-3.7.0, benchmark-4.0.0, mock-3.12.0 347s collected 551 items 347s 347s tests/test_core/test_configuration.py ...... [ 1%] 353s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 354s ...................x....... [ 12%] 354s tests/test_core/test_dictlist.py ...................... [ 16%] 354s tests/test_core/test_formula.py ..... [ 17%] 354s tests/test_core/test_gene.py . [ 17%] 354s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 366s .......................... [ 29%] 366s tests/test_core/test_group.py .. [ 30%] 366s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 375s tests/test_core/test_model.py .......................................... [ 39%] 376s ...........s..s.ss. [ 43%] 376s tests/test_core/test_solution.py .ss [ 43%] 384s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 386s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 390s tests/test_flux_analysis/test_geometric.py .. [ 46%] 391s tests/test_flux_analysis/test_moma.py . [ 46%] 395s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 395s tests/test_flux_analysis/test_reaction.py . [ 47%] 399s tests/test_flux_analysis/test_room.py .... [ 47%] 404s tests/test_flux_analysis/test_variability.py ....... [ 49%] 404s tests/test_flux_analysis/test_deletion.py sss [ 49%] 404s tests/test_flux_analysis/test_moma.py s [ 49%] 408s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 411s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 411s tests/test_flux_analysis/test_helpers.py ... [ 51%] 412s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 416s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 416s tests/test_flux_analysis/test_variability.py ....... [ 54%] 416s tests/test_io/test_annotation.py .. [ 55%] 416s tests/test_io/test_annotation_format.py .. [ 55%] 421s tests/test_io/test_io_order.py ........................... [ 60%] 421s tests/test_io/test_json.py .... [ 61%] 442s tests/test_io/test_mat.py ............... [ 64%] 442s tests/test_io/test_notes.py . [ 64%] 442s tests/test_io/test_pickle.py .. [ 64%] 451s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 451s tests/test_io/test_yaml.py .x [ 72%] 451s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 451s tests/test_manipulation/test_annotate.py . [ 73%] 452s tests/test_manipulation/test_delete.py ....... [ 75%] 452s tests/test_manipulation/test_modify.py ... [ 75%] 452s tests/test_manipulation/test_validate.py .. [ 76%] 453s tests/test_medium/test_boundary_types.py ......... [ 77%] 455s tests/test_medium/test_minimal_medium.py .......... [ 79%] 457s tests/test_sampling/test_achr.py ...... [ 80%] 460s tests/test_sampling/test_optgp.py ...... [ 81%] 468s tests/test_sampling/test_sampling.py .......... [ 83%] 470s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 472s tests/test_summary/test_model_summary.py ............... [ 89%] 474s tests/test_summary/test_reaction_summary.py .................... [ 92%] 474s tests/test_util/test_array.py .. [ 93%] 474s tests/test_util/test_context.py ... [ 93%] 474s tests/test_util/test_process_pool.py ............... [ 96%] 475s tests/test_util/test_solver.py ..............s [ 99%] 475s tests/test_util/test_util.py ...X [100%] 475s 475s =============================== warnings summary =============================== 475s ../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 475s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 475s EPOCH = datetime.datetime.utcfromtimestamp(0) 475s 475s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 475s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 475s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 475s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 475s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(591001.3.peg.1891 AND 591001.3.peg.1892 AND 591001.3.peg.1893)'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 475s warn( 475s 475s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 475s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 475s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 475s warn( 475s 475s tests/test_core/test_model.py::test_reaction_delete 475s tests/test_core/test_model.py::test_reaction_delete 475s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 475s warn( 475s 475s tests/test_core/test_model.py::test_group_loss_of_elements 475s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 475s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 475s warn("need to pass in a list") 475s 475s tests/test_core/test_model.py::test_change_objective 475s tests/test_core/test_model.py::test_change_objective 475s tests/test_core/test_model.py::test_change_objective 475s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 475s warn("Please use reaction.flux instead.", DeprecationWarning) 475s 475s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 475s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 475s /tmp/autopkgtest.ssAppb/autopkgtest_tmp/tests/test_flux_analysis/test_deletion.py:438: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead 475s assert math.isnan(sol.growth) 475s 475s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 475s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 475s /tmp/autopkgtest.ssAppb/autopkgtest_tmp/tests/test_flux_analysis/test_deletion.py:439: FutureWarning: Calling float on a single element Series is deprecated and will raise a TypeError in the future. Use float(ser.iloc[0]) instead 475s assert math.isnan(sol_one.growth) 475s 475s tests/test_io/test_json.py: 1 warning 475s tests/test_io/test_mat.py: 5 warnings 475s tests/test_io/test_pickle.py: 1 warning 475s tests/test_io/test_sbml.py: 9 warnings 475s tests/test_io/test_yaml.py: 1 warning 475s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 475s warn(f"Solver status is '{status}'.", UserWarning) 475s 475s tests/test_medium/test_boundary_types.py: 96 warnings 475s /usr/lib/python3/dist-packages/cobra/medium/boundary_types.py:97: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 475s return most[0] 475s 475s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 475s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 475s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 475s /usr/lib/python3/dist-packages/cobra/medium/boundary_types.py:74: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 475s compartment = most[matches[most]][0] 475s 475s tests/test_util/test_process_pool.py::test_with_context 475s /usr/lib/python3/dist-packages/cobra/util/process_pool.py:72: PytestMockWarning: Mocks returned by pytest-mock do not need to be used as context managers. The mocker fixture automatically undoes mocking at the end of a test. This warning can be ignored if it was triggered by mocking a context manager. https://pytest-mock.readthedocs.io/en/latest/remarks.html#usage-as-context-manager 475s self._pool.__enter__() 475s 475s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 475s 475s -------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests --------------------------------------------------------------------------------------------------------------------- 475s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 475s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 475s test_subtract_metabolite_benchmark[gurobi] 5.2680 (1.0) 65.7050 (2.72) 5.5641 (1.00) 1.1033 (2.00) 5.4690 (1.0) 0.1145 (1.18) 27;525 179,723.3804 (1.00) 4608 1 475s test_subtract_metabolite_benchmark[cplex] 5.2870 (1.00) 24.1870 (1.0) 5.5443 (1.0) 0.5529 (1.0) 5.4860 (1.00) 0.0970 (1.0) 61;335 180,366.2475 (1.0) 4283 1 475s test_subtract_metabolite_benchmark[glpk] 5.3030 (1.01) 91.6720 (3.79) 5.6546 (1.02) 1.8353 (3.32) 5.5290 (1.01) 0.1340 (1.38) 24;613 176,846.2709 (0.98) 4654 1 475s test_achr_sample_benchmark 251.3320 (47.71) 661.7350 (27.36) 262.2077 (47.29) 19.2422 (34.80) 257.2660 (47.04) 9.5298 (98.24) 50;67 3,813.7699 (0.02) 1603 1 475s test_change_objective_benchmark[optlang-glpk] 259.8100 (49.32) 1,625.4040 (67.20) 284.5712 (51.33) 54.5569 (98.67) 266.1325 (48.66) 19.6795 (202.88) 154;245 3,514.0591 (0.02) 1924 1 475s test_optgp_sample_benchmark 391.8850 (74.39) 792.3940 (32.76) 409.7293 (73.90) 26.2983 (47.56) 401.5820 (73.43) 17.6162 (181.61) 154;116 2,440.6357 (0.01) 1773 1 475s test_loopless_benchmark_after 1,248.1920 (236.94) 1,511.8270 (62.51) 1,290.3826 (232.74) 37.7069 (68.20) 1,278.7110 (233.81) 28.1975 (290.70) 28;20 774.9639 (0.00) 316 1 475s test_single_gene_deletion_fba_benchmark[glpk] 4,537.8680 (861.40) 5,678.1560 (234.76) 4,690.5225 (846.01) 154.7660 (279.92) 4,648.0470 (849.89) 152.3305 (>1000.0) 22;10 213.1959 (0.00) 181 1 475s test_minimal_medium_mip_benchmark 6,921.5650 (>1000.0) 8,316.0740 (343.82) 7,117.3524 (>1000.0) 220.2189 (398.30) 7,043.9720 (>1000.0) 174.4735 (>1000.0) 8;5 140.5017 (0.00) 79 1 475s test_minimal_medium_linear_benchmark 6,992.8810 (>1000.0) 7,649.4140 (316.26) 7,142.8697 (>1000.0) 115.3282 (208.59) 7,117.9015 (>1000.0) 89.5525 (923.22) 11;5 139.9998 (0.00) 76 1 475s test_loopless_benchmark_before 7,592.4770 (>1000.0) 8,493.1970 (351.15) 7,841.5926 (>1000.0) 187.1438 (338.48) 7,790.0520 (>1000.0) 220.0817 (>1000.0) 15;3 127.5251 (0.00) 75 1 475s test_copy_benchmark[optlang-glpk] 22,316.0800 (>1000.0) 169,031.9800 (>1000.0) 27,036.6329 (>1000.0) 21,922.1624 (>1000.0) 23,869.8520 (>1000.0) 1,252.8420 (>1000.0) 1;2 36.9869 (0.00) 44 1 475s test_flux_variability_loopless_benchmark[glpk] 29,136.3260 (>1000.0) 40,003.0560 (>1000.0) 30,615.5372 (>1000.0) 2,842.7710 (>1000.0) 29,890.8110 (>1000.0) 524.3403 (>1000.0) 1;1 32.6632 (0.00) 13 1 475s test_single_reaction_deletion_benchmark[glpk] 31,798.2010 (>1000.0) 39,264.0110 (>1000.0) 35,326.7987 (>1000.0) 1,870.9721 (>1000.0) 35,646.1545 (>1000.0) 2,073.2270 (>1000.0) 11;0 28.3071 (0.00) 30 1 475s test_gpr_equality_benchmark 34,656.0860 (>1000.0) 36,623.8620 (>1000.0) 35,264.3903 (>1000.0) 462.2246 (836.01) 35,144.3800 (>1000.0) 506.6000 (>1000.0) 5;2 28.3572 (0.00) 26 1 475s test_deepcopy_benchmark 35,328.5210 (>1000.0) 44,893.7360 (>1000.0) 38,556.3591 (>1000.0) 2,073.0192 (>1000.0) 38,108.5290 (>1000.0) 2,122.6975 (>1000.0) 5;1 25.9361 (0.00) 25 1 475s test_double_reaction_deletion_benchmark 60,407.6280 (>1000.0) 64,774.6980 (>1000.0) 61,450.4612 (>1000.0) 1,863.5063 (>1000.0) 60,661.4650 (>1000.0) 1,227.6653 (>1000.0) 1;1 16.2733 (0.00) 5 1 475s test_fastcc_benchmark[glpk] 81,769.3170 (>1000.0) 99,924.3450 (>1000.0) 92,507.2602 (>1000.0) 5,905.1540 (>1000.0) 92,086.0790 (>1000.0) 8,201.2442 (>1000.0) 4;0 10.8100 (0.00) 11 1 475s test_add_metabolite_benchmark[glpk] 100,153.1340 (>1000.0) 103,313.2080 (>1000.0) 100,695.2656 (>1000.0) 946.5493 (>1000.0) 100,435.8105 (>1000.0) 417.4310 (>1000.0) 1;1 9.9310 (0.00) 10 1 475s test_add_metabolite_benchmark[gurobi] 100,561.5170 (>1000.0) 110,729.7870 (>1000.0) 105,296.7133 (>1000.0) 3,885.0946 (>1000.0) 104,919.8890 (>1000.0) 7,945.3350 (>1000.0) 5;0 9.4970 (0.00) 10 1 475s test_add_metabolite_benchmark[cplex] 106,542.6160 (>1000.0) 110,828.6540 (>1000.0) 109,089.1059 (>1000.0) 1,568.1096 (>1000.0) 109,898.3270 (>1000.0) 2,380.1650 (>1000.0) 4;0 9.1668 (0.00) 11 1 475s test_optgp_init_benchmark 109,262.1940 (>1000.0) 115,478.1550 (>1000.0) 112,310.2053 (>1000.0) 2,115.9359 (>1000.0) 111,784.4760 (>1000.0) 2,643.9392 (>1000.0) 3;0 8.9039 (0.00) 9 1 475s test_achr_init_benchmark 111,345.0090 (>1000.0) 118,301.4310 (>1000.0) 113,659.2644 (>1000.0) 2,172.2999 (>1000.0) 113,468.8820 (>1000.0) 2,691.8850 (>1000.0) 2;0 8.7982 (0.00) 9 1 475s test_double_gene_deletion_benchmark 198,826.5560 (>1000.0) 217,782.3980 (>1000.0) 206,220.8058 (>1000.0) 7,829.2473 (>1000.0) 202,107.2520 (>1000.0) 11,440.4812 (>1000.0) 1;0 4.8492 (0.00) 5 1 475s test_single_gene_deletion_linear_moma_benchmark[glpk] 263,683.1520 (>1000.0) 267,656.7800 (>1000.0) 266,318.7074 (>1000.0) 1,709.8989 (>1000.0) 267,177.5760 (>1000.0) 2,539.4188 (>1000.0) 1;0 3.7549 (0.00) 5 1 475s test_gpr_symbolism_benchmark 267,810.1330 (>1000.0) 282,601.1790 (>1000.0) 272,410.0794 (>1000.0) 5,855.4416 (>1000.0) 270,774.6000 (>1000.0) 5,051.2137 (>1000.0) 1;1 3.6709 (0.00) 5 1 475s test_pfba_benchmark[glpk] 345,742.9080 (>1000.0) 478,049.9060 (>1000.0) 372,888.0756 (>1000.0) 58,789.6588 (>1000.0) 347,040.5240 (>1000.0) 33,446.0720 (>1000.0) 1;1 2.6818 (0.00) 5 1 475s test_flux_variability_benchmark[glpk] 390,341.8630 (>1000.0) 396,767.2540 (>1000.0) 393,197.4150 (>1000.0) 2,644.0769 (>1000.0) 393,925.7570 (>1000.0) 4,092.8145 (>1000.0) 2;0 2.5433 (0.00) 5 1 475s test_single_gene_deletion_linear_room_benchmark[glpk] 414,936.7870 (>1000.0) 461,320.3050 (>1000.0) 432,251.4976 (>1000.0) 18,252.9630 (>1000.0) 425,950.8110 (>1000.0) 23,842.6872 (>1000.0) 1;0 2.3135 (0.00) 5 1 475s test_copy_benchmark_large_model[optlang-glpk] 438,082.7840 (>1000.0) 647,153.6040 (>1000.0) 517,471.5332 (>1000.0) 108,704.1648 (>1000.0) 438,479.5660 (>1000.0) 192,559.1365 (>1000.0) 1;0 1.9325 (0.00) 5 1 475s test_geometric_fba_benchmark[glpk] 535,043.8590 (>1000.0) 553,200.4240 (>1000.0) 542,114.3822 (>1000.0) 7,291.2579 (>1000.0) 542,846.5810 (>1000.0) 10,146.6760 (>1000.0) 1;0 1.8446 (0.00) 5 1 475s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 475s 475s Legend: 475s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 475s OPS: Operations Per Second, computed as 1 / Mean 475s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 172 warnings in 129.73s (0:02:09) = 476s Removing patch debian/patches/no_future_dependency.patch 476s Restoring setup.cfg 476s 476s Removing patch debian/patches/32-bit-test.patch 476s Restoring tests/test_io/test_mat.py 476s 476s Removing patch debian/patches/do-not-seek-for-name.patch 476s Restoring src/cobra/io/sbml.py 476s 476s Removing patch debian/patches/ignore_tests.patch 476s Restoring tests/test_io/test_web/test_load.py 476s 476s Removing patch debian/patches/xfail_test_show_versions.patch 476s Restoring tests/test_util/test_util.py 476s 476s Removing patch debian/patches/mathjax.patch 476s Restoring documentation_builder/conf.py 476s 476s No patches applied 476s PASS 477s autopkgtest [10:51:20]: test run-unit-test: -----------------------] 477s autopkgtest [10:51:20]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 477s run-unit-test PASS 478s autopkgtest [10:51:21]: @@@@@@@@@@@@@@@@@@@@ summary 478s run-unit-test PASS 505s Creating nova instance adt-noble-ppc64el-python-cobra-20240326-104323-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240325.img (UUID ce50e202-ac12-4562-879d-419903f0141e)...