0s autopkgtest [04:15:07]: starting date and time: 2024-05-06 04:15:07+0000 0s autopkgtest [04:15:07]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [04:15:07]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.czuhtpqb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml,src:monty,src:ruamel.yaml.clib --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 monty/2024.4.17-1 ruamel.yaml.clib/0.2.8+ds-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-20.secgroup --name adt-oracular-ppc64el-python-cobra-20240506-041506-juju-7f2275-prod-proposed-migration-environment-2-a3fccc2e-a66d-4909-86a4-b1d429a8699e --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 311s autopkgtest [04:20:18]: testbed dpkg architecture: ppc64el 311s autopkgtest [04:20:18]: testbed apt version: 2.7.14build2 311s autopkgtest [04:20:18]: @@@@@@@@@@@@@@@@@@@@ test bed setup 312s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 312s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 313s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [110 kB] 313s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1647 kB] 313s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 313s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [182 kB] 313s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1260 B] 313s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [1269 kB] 313s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [22.6 kB] 313s Fetched 3322 kB in 1s (2608 kB/s) 313s Reading package lists... 316s Reading package lists... 316s Building dependency tree... 316s Reading state information... 316s Calculating upgrade... 317s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 317s Reading package lists... 317s Building dependency tree... 317s Reading state information... 317s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 318s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 318s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 318s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 318s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 319s Reading package lists... 319s Reading package lists... 319s Building dependency tree... 319s Reading state information... 319s Calculating upgrade... 320s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 320s Reading package lists... 320s Building dependency tree... 320s Reading state information... 320s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 323s autopkgtest [04:20:30]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 323s autopkgtest [04:20:30]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 325s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 325s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 325s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 325s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 325s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 325s gpgv: Can't check signature: No public key 325s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 326s autopkgtest [04:20:33]: testing package python-cobra version 0.29.0-1ubuntu2 326s autopkgtest [04:20:33]: build not needed 327s autopkgtest [04:20:34]: test run-unit-test: preparing testbed 328s Reading package lists... 328s Building dependency tree... 328s Reading state information... 329s Starting pkgProblemResolver with broken count: 0 329s Starting 2 pkgProblemResolver with broken count: 0 329s Done 329s The following additional packages will be installed: 329s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 329s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 329s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 329s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 329s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 329s python3-importlib-resources python3-iniconfig python3-more-itertools 329s python3-mpmath python3-numpy python3-optlang python3-packaging 329s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 329s python3-pytest python3-pytest-benchmark python3-pytest-mock 329s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 329s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 329s python3-tabulate python3-zipp quilt swig 329s Suggested packages: 329s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 329s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 329s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 329s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 329s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 329s swig-doc swig-examples 329s Recommended packages: 329s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 329s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 329s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 329s python3-pil isympy-common 329s The following NEW packages will be installed: 329s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 329s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 329s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 329s python3-click python3-cobra python3-colorama python3-cpuinfo 329s python3-dateutil python3-decorator python3-depinfo python3-diskcache 329s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 329s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 329s python3-optlang python3-packaging python3-pandas python3-pandas-lib 329s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 329s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 329s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 329s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 329s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 329s Need to get 53.0 MB/53.0 MB of archives. 329s After this operation, 265 MB of additional disk space will be used. 329s Get:1 /tmp/autopkgtest.cH4z25/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [768 B] 329s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el diffstat ppc64el 1.66-1build1 [33.0 kB] 329s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB] 330s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el gettext ppc64el 0.21-14ubuntu2 [985 kB] 330s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsuitesparseconfig7 ppc64el 1:7.6.1+dfsg-1build1 [12.9 kB] 330s Get:6 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libamd3 ppc64el 1:7.6.1+dfsg-1build1 [36.6 kB] 330s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 330s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcolamd3 ppc64el 1:7.6.1+dfsg-1build1 [21.6 kB] 330s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14-20240412-0ubuntu1 [574 kB] 330s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el libltdl7 ppc64el 2.4.7-7build1 [48.2 kB] 330s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libglpk40 ppc64el 5.0-1build2 [467 kB] 330s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 330s Get:13 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 330s Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpython3.12t64 ppc64el 3.12.3-1 [2553 kB] 330s Get:15 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 330s Get:16 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sniffio all 1.3.0-2 [7216 B] 330s Get:17 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-anyio all 4.2.0-1 [56.5 kB] 330s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 330s Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 330s Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-click all 8.1.6-2 [79.0 kB] 330s Get:21 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-depinfo ppc64el 2.2.0-2 [10.9 kB] 330s Get:22 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-diskcache all 5.6.3-1 [35.1 kB] 330s Get:23 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-h11 all 0.14.0-1 [51.1 kB] 330s Get:24 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-httpcore all 1.0.4-1 [38.8 kB] 330s Get:25 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-httpx all 0.26.0-2 [61.3 kB] 330s Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-more-itertools all 10.2.0-1 [52.9 kB] 330s Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-zipp all 1.0.0-6 [6090 B] 330s Get:28 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-importlib-resources all 6.0.1-1 [22.1 kB] 330s Get:29 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-6ubuntu1 [4446 kB] 330s Get:30 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-swiglpk ppc64el 5.0.10-1build1 [85.0 kB] 330s Get:31 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-mpmath all 1.2.1-3 [421 kB] 330s Get:32 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sympy all 1.12-7 [3966 kB] 330s Get:33 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-optlang all 1.8.1-1 [82.7 kB] 330s Get:34 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 330s Get:35 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-7 [4602 kB] 330s Get:36 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pandas all 2.1.4+dfsg-7 [3042 kB] 330s Get:37 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-pydantic ppc64el 1.10.14-1 [1825 kB] 330s Get:38 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-ruamel.yaml.clib ppc64el 0.2.8+ds-1 [158 kB] 330s Get:39 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 330s Get:40 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-simplejson ppc64el 3.19.2-1build2 [60.6 kB] 331s Get:41 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-tabulate all 0.8.10-1 [38.2 kB] 331s Get:42 http://ftpmaster.internal/ubuntu oracular/universe ppc64el swig ppc64el 4.2.0-2ubuntu1 [1261 kB] 331s Get:43 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sbml5 ppc64el 5.20.2+dfsg-3 [3752 kB] 331s Get:44 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cobra ppc64el 0.29.0-1ubuntu2 [1119 kB] 331s Get:45 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cpuinfo all 9.0.0-1 [21.2 kB] 331s Get:46 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 331s Get:47 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 331s Get:48 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.0-1 [41.1 kB] 331s Get:49 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB] 331s Get:50 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 331s Get:51 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 331s Get:52 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 331s Get:53 http://ftpmaster.internal/ubuntu oracular/universe ppc64el quilt all 0.67+really0.67-4 [436 kB] 331s Get:54 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-scipy ppc64el 1.11.4-6build1 [17.0 MB] 331s Fetched 53.0 MB in 2s (26.5 MB/s) 332s Selecting previously unselected package diffstat. 332s (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 ... 72141 files and directories currently installed.) 332s Preparing to unpack .../00-diffstat_1.66-1build1_ppc64el.deb ... 332s Unpacking diffstat (1.66-1build1) ... 332s Selecting previously unselected package libgomp1:ppc64el. 332s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_ppc64el.deb ... 332s Unpacking libgomp1:ppc64el (14-20240412-0ubuntu1) ... 332s Selecting previously unselected package gettext. 332s Preparing to unpack .../02-gettext_0.21-14ubuntu2_ppc64el.deb ... 332s Unpacking gettext (0.21-14ubuntu2) ... 332s Selecting previously unselected package libsuitesparseconfig7:ppc64el. 332s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 332s Unpacking libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1build1) ... 332s Selecting previously unselected package libamd3:ppc64el. 332s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 332s Unpacking libamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 332s Selecting previously unselected package libblas3:ppc64el. 332s Preparing to unpack .../05-libblas3_3.12.0-3build1_ppc64el.deb ... 332s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 332s Selecting previously unselected package libcolamd3:ppc64el. 332s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 332s Unpacking libcolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 332s Selecting previously unselected package libgfortran5:ppc64el. 332s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_ppc64el.deb ... 332s Unpacking libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 332s Selecting previously unselected package libltdl7:ppc64el. 332s Preparing to unpack .../08-libltdl7_2.4.7-7build1_ppc64el.deb ... 332s Unpacking libltdl7:ppc64el (2.4.7-7build1) ... 332s Selecting previously unselected package libglpk40:ppc64el. 332s Preparing to unpack .../09-libglpk40_5.0-1build2_ppc64el.deb ... 332s Unpacking libglpk40:ppc64el (5.0-1build2) ... 332s Selecting previously unselected package liblapack3:ppc64el. 332s Preparing to unpack .../10-liblapack3_3.12.0-3build1_ppc64el.deb ... 332s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 332s Selecting previously unselected package liblbfgsb0:ppc64el. 332s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 332s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 332s Selecting previously unselected package libpython3.12t64:ppc64el. 332s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_ppc64el.deb ... 332s Unpacking libpython3.12t64:ppc64el (3.12.3-1) ... 332s Selecting previously unselected package python-cobra-data. 332s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 332s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 332s Selecting previously unselected package python3-sniffio. 332s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 332s Unpacking python3-sniffio (1.3.0-2) ... 332s Selecting previously unselected package python3-anyio. 332s Preparing to unpack .../15-python3-anyio_4.2.0-1_all.deb ... 332s Unpacking python3-anyio (4.2.0-1) ... 332s Selecting previously unselected package python3-appdirs. 332s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 332s Unpacking python3-appdirs (1.4.4-4) ... 332s Selecting previously unselected package python3-colorama. 332s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 332s Unpacking python3-colorama (0.4.6-4) ... 332s Selecting previously unselected package python3-click. 332s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 332s Unpacking python3-click (8.1.6-2) ... 332s Selecting previously unselected package python3-depinfo. 332s Preparing to unpack .../19-python3-depinfo_2.2.0-2_ppc64el.deb ... 332s Unpacking python3-depinfo (2.2.0-2) ... 332s Selecting previously unselected package python3-diskcache. 332s Preparing to unpack .../20-python3-diskcache_5.6.3-1_all.deb ... 332s Unpacking python3-diskcache (5.6.3-1) ... 332s Selecting previously unselected package python3-h11. 332s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 332s Unpacking python3-h11 (0.14.0-1) ... 332s Selecting previously unselected package python3-httpcore. 332s Preparing to unpack .../22-python3-httpcore_1.0.4-1_all.deb ... 332s Unpacking python3-httpcore (1.0.4-1) ... 332s Selecting previously unselected package python3-httpx. 332s Preparing to unpack .../23-python3-httpx_0.26.0-2_all.deb ... 332s Unpacking python3-httpx (0.26.0-2) ... 332s Selecting previously unselected package python3-more-itertools. 332s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 332s Unpacking python3-more-itertools (10.2.0-1) ... 332s Selecting previously unselected package python3-zipp. 332s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 332s Unpacking python3-zipp (1.0.0-6) ... 332s Selecting previously unselected package python3-importlib-resources. 332s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 332s Unpacking python3-importlib-resources (6.0.1-1) ... 332s Selecting previously unselected package python3-numpy. 332s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_ppc64el.deb ... 332s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 333s Selecting previously unselected package python3-swiglpk. 333s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_ppc64el.deb ... 333s Unpacking python3-swiglpk (5.0.10-1build1) ... 333s Selecting previously unselected package python3-mpmath. 333s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 333s Unpacking python3-mpmath (1.2.1-3) ... 333s Selecting previously unselected package python3-sympy. 333s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 333s Unpacking python3-sympy (1.12-7) ... 333s Selecting previously unselected package python3-optlang. 333s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 333s Unpacking python3-optlang (1.8.1-1) ... 333s Selecting previously unselected package python3-dateutil. 333s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 333s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 333s Selecting previously unselected package python3-pandas-lib:ppc64el. 333s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_ppc64el.deb ... 333s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-7) ... 333s Selecting previously unselected package python3-pandas. 333s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 333s Unpacking python3-pandas (2.1.4+dfsg-7) ... 334s Selecting previously unselected package python3-pydantic. 334s Preparing to unpack .../35-python3-pydantic_1.10.14-1_ppc64el.deb ... 334s Unpacking python3-pydantic (1.10.14-1) ... 334s Selecting previously unselected package python3-ruamel.yaml.clib:ppc64el. 334s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8+ds-1_ppc64el.deb ... 334s Unpacking python3-ruamel.yaml.clib:ppc64el (0.2.8+ds-1) ... 334s Selecting previously unselected package python3-ruamel.yaml. 334s Preparing to unpack .../37-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 334s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 334s Selecting previously unselected package python3-simplejson. 334s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_ppc64el.deb ... 334s Unpacking python3-simplejson (3.19.2-1build2) ... 334s Selecting previously unselected package python3-tabulate. 334s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 334s Unpacking python3-tabulate (0.8.10-1) ... 334s Selecting previously unselected package swig. 334s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_ppc64el.deb ... 334s Unpacking swig (4.2.0-2ubuntu1) ... 334s Selecting previously unselected package python3-sbml5. 334s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_ppc64el.deb ... 334s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 334s Selecting previously unselected package python3-cobra. 334s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_ppc64el.deb ... 334s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 334s Selecting previously unselected package python3-cpuinfo. 334s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 334s Unpacking python3-cpuinfo (9.0.0-1) ... 334s Selecting previously unselected package python3-decorator. 334s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 334s Unpacking python3-decorator (5.1.1-5) ... 334s Selecting previously unselected package python3-iniconfig. 334s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 334s Unpacking python3-iniconfig (1.1.1-2) ... 334s Selecting previously unselected package python3-packaging. 334s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 334s Unpacking python3-packaging (24.0-1) ... 334s Selecting previously unselected package python3-pluggy. 334s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 334s Unpacking python3-pluggy (1.4.0-1) ... 334s Selecting previously unselected package python3-pytest. 334s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 334s Unpacking python3-pytest (7.4.4-1) ... 334s Selecting previously unselected package python3-pytest-benchmark. 334s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 334s Unpacking python3-pytest-benchmark (4.0.0-3) ... 335s Selecting previously unselected package python3-pytest-mock. 335s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 335s Unpacking python3-pytest-mock (3.12.0-1.1) ... 335s Selecting previously unselected package quilt. 335s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 335s Unpacking quilt (0.67+really0.67-4) ... 335s Selecting previously unselected package python3-scipy. 335s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_ppc64el.deb ... 335s Unpacking python3-scipy (1.11.4-6build1) ... 335s Selecting previously unselected package autopkgtest-satdep. 335s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 335s Unpacking autopkgtest-satdep (0) ... 335s Setting up python3-more-itertools (10.2.0-1) ... 336s Setting up python3-iniconfig (1.1.1-2) ... 336s Setting up python3-sniffio (1.3.0-2) ... 336s Setting up swig (4.2.0-2ubuntu1) ... 336s Setting up python3-anyio (4.2.0-1) ... 336s Setting up python3-colorama (0.4.6-4) ... 336s Setting up python3-ruamel.yaml.clib:ppc64el (0.2.8+ds-1) ... 336s Setting up python3-tabulate (0.8.10-1) ... 336s Setting up python3-zipp (1.0.0-6) ... 336s Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ... 336s Setting up python3-click (8.1.6-2) ... 337s Setting up libpython3.12t64:ppc64el (3.12.3-1) ... 337s Setting up python3-simplejson (3.19.2-1build2) ... 337s Setting up python3-decorator (5.1.1-5) ... 337s Setting up libblas3:ppc64el (3.12.0-3build1) ... 337s 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 337s Setting up python3-packaging (24.0-1) ... 337s Setting up python3-pydantic (1.10.14-1) ... 338s Setting up diffstat (1.66-1build1) ... 338s Setting up python3-h11 (0.14.0-1) ... 338s Setting up python3-depinfo (2.2.0-2) ... 338s Setting up python3-cpuinfo (9.0.0-1) ... 338s Setting up libltdl7:ppc64el (2.4.7-7build1) ... 338s Setting up libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 338s Setting up python3-pluggy (1.4.0-1) ... 338s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 338s Setting up libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1build1) ... 338s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 339s Setting up python3-mpmath (1.2.1-3) ... 339s Setting up python3-diskcache (5.6.3-1) ... 340s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 340s Setting up python3-appdirs (1.4.4-4) ... 340s Setting up python3-httpcore (1.0.4-1) ... 340s Setting up python3-sympy (1.12-7) ... 347s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 347s 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 347s Setting up gettext (0.21-14ubuntu2) ... 347s Setting up libamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 347s Setting up python3-importlib-resources (6.0.1-1) ... 347s Setting up libcolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 347s Setting up python3-pytest (7.4.4-1) ... 348s Setting up quilt (0.67+really0.67-4) ... 348s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 348s Setting up python3-httpx (0.26.0-2) ... 348s Setting up libglpk40:ppc64el (5.0-1build2) ... 348s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 351s Setting up python3-pytest-mock (3.12.0-1.1) ... 351s Setting up python3-swiglpk (5.0.10-1build1) ... 351s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 351s Setting up python3-optlang (1.8.1-1) ... 351s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 351s """A representation of the convex optimizatgion problem in standard form. 351s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 351s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 351s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 351s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 351s Setting up python3-pytest-benchmark (4.0.0-3) ... 352s Setting up python3-scipy (1.11.4-6build1) ... 356s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-7) ... 356s Setting up python3-pandas (2.1.4+dfsg-7) ... 362s Setting up python3-cobra (0.29.0-1ubuntu2) ... 362s Setting up autopkgtest-satdep (0) ... 362s Processing triggers for man-db (2.12.0-4build2) ... 362s Processing triggers for install-info (7.1-3build2) ... 363s Processing triggers for libc-bin (2.39-0ubuntu8) ... 367s (Reading database ... 80170 files and directories currently installed.) 367s Removing autopkgtest-satdep (0) ... 367s autopkgtest [04:21:14]: test run-unit-test: [----------------------- 367s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 367s Running Tests 367s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 371s ============================= test session starts ============================== 371s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 371s 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) 371s rootdir: /tmp/autopkgtest.cH4z25/autopkgtest_tmp 371s plugins: mock-3.12.0, benchmark-4.0.0, anyio-4.2.0 371s collected 551 items 371s 371s tests/test_core/test_configuration.py ...... [ 1%] 377s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 379s ...................x....... [ 12%] 379s tests/test_core/test_dictlist.py ...................... [ 16%] 379s tests/test_core/test_formula.py ..... [ 17%] 379s tests/test_core/test_gene.py . [ 17%] 379s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 392s .......................... [ 29%] 392s tests/test_core/test_group.py .. [ 30%] 392s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 403s tests/test_core/test_model.py .......................................... [ 39%] 403s ...........s..s.ss. [ 43%] 403s tests/test_core/test_solution.py .ss [ 43%] 411s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 413s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 417s tests/test_flux_analysis/test_geometric.py .. [ 46%] 418s tests/test_flux_analysis/test_moma.py . [ 46%] 423s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 423s tests/test_flux_analysis/test_reaction.py . [ 47%] 426s tests/test_flux_analysis/test_room.py .... [ 47%] 431s tests/test_flux_analysis/test_variability.py ....... [ 49%] 432s tests/test_flux_analysis/test_deletion.py sss [ 49%] 432s tests/test_flux_analysis/test_moma.py s [ 49%] 437s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 440s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 440s tests/test_flux_analysis/test_helpers.py ... [ 51%] 441s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 444s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 446s tests/test_flux_analysis/test_variability.py ....... [ 54%] 446s tests/test_io/test_annotation.py .. [ 55%] 446s tests/test_io/test_annotation_format.py .. [ 55%] 451s tests/test_io/test_io_order.py ........................... [ 60%] 451s tests/test_io/test_json.py .... [ 61%] 476s tests/test_io/test_mat.py ............... [ 64%] 476s tests/test_io/test_notes.py . [ 64%] 476s tests/test_io/test_pickle.py .. [ 64%] 485s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 486s tests/test_io/test_yaml.py .x [ 72%] 486s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 487s tests/test_manipulation/test_annotate.py . [ 73%] 487s tests/test_manipulation/test_delete.py ....... [ 75%] 488s tests/test_manipulation/test_modify.py ... [ 75%] 488s tests/test_manipulation/test_validate.py .. [ 76%] 488s tests/test_medium/test_boundary_types.py ......... [ 77%] 490s tests/test_medium/test_minimal_medium.py .......... [ 79%] 493s tests/test_sampling/test_achr.py ...... [ 80%] 495s tests/test_sampling/test_optgp.py ...... [ 81%] 505s tests/test_sampling/test_sampling.py .......... [ 83%] 506s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 508s tests/test_summary/test_model_summary.py ............... [ 89%] 510s tests/test_summary/test_reaction_summary.py .................... [ 92%] 510s tests/test_util/test_array.py .. [ 93%] 510s tests/test_util/test_context.py ... [ 93%] 511s tests/test_util/test_process_pool.py ............... [ 96%] 512s tests/test_util/test_solver.py ..............s [ 99%] 512s tests/test_util/test_util.py ...X [100%] 512s 512s =============================== warnings summary =============================== 512s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 512s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 512s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 512s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 512s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 512s /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)'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 512s warn( 512s 512s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 512s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 512s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 512s warn( 512s 512s tests/test_core/test_model.py::test_reaction_delete 512s tests/test_core/test_model.py::test_reaction_delete 512s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 512s warn( 512s 512s tests/test_core/test_model.py::test_group_loss_of_elements 512s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 512s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 512s warn("need to pass in a list") 512s 512s tests/test_core/test_model.py::test_change_objective 512s tests/test_core/test_model.py::test_change_objective 512s tests/test_core/test_model.py::test_change_objective 512s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 512s warn("Please use reaction.flux instead.", DeprecationWarning) 512s 512s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 512s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 512s /tmp/autopkgtest.cH4z25/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 512s assert math.isnan(sol.growth) 512s 512s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 512s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 512s /tmp/autopkgtest.cH4z25/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 512s assert math.isnan(sol_one.growth) 512s 512s tests/test_io/test_json.py: 1 warning 512s tests/test_io/test_mat.py: 5 warnings 512s tests/test_io/test_pickle.py: 1 warning 512s tests/test_io/test_sbml.py: 9 warnings 512s tests/test_io/test_yaml.py: 1 warning 512s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 512s warn(f"Solver status is '{status}'.", UserWarning) 512s 512s tests/test_io/test_yaml.py::test_save_yaml_model 512s /tmp/autopkgtest.cH4z25/autopkgtest_tmp/tests/test_io/test_yaml.py:29: PendingDeprecationWarning: 512s you should no longer specify 'unsafe'. 512s For **dumping only** use yaml=YAML(typ='full') 512s 512s yaml = YAML(typ="unsafe") 512s 512s tests/test_medium/test_boundary_types.py: 96 warnings 512s /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]` 512s return most[0] 512s 512s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 512s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 512s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 512s /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]` 512s compartment = most[matches[most]][0] 512s 512s tests/test_util/test_process_pool.py::test_with_context 512s /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 512s self._pool.__enter__() 512s 512s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 512s 512s -------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests --------------------------------------------------------------------------------------------------------------------- 512s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 512s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 512s test_subtract_metabolite_benchmark[glpk] 6.4900 (1.0) 122.7190 (1.27) 7.0590 (1.0) 1.9917 (1.25) 6.9405 (1.0) 0.4520 (1.0) 17;26 141,663.9456 (1.0) 3742 1 512s test_subtract_metabolite_benchmark[gurobi] 6.6020 (1.02) 96.6010 (1.0) 7.1473 (1.01) 1.5950 (1.0) 7.0140 (1.01) 0.4657 (1.03) 20;29 139,913.8783 (0.99) 3999 1 512s test_subtract_metabolite_benchmark[cplex] 6.6040 (1.02) 97.8270 (1.01) 7.1765 (1.02) 2.1999 (1.38) 7.0330 (1.01) 0.4650 (1.03) 19;32 139,343.5478 (0.98) 3792 1 512s test_achr_sample_benchmark 269.8160 (41.57) 433.3070 (4.49) 304.2373 (43.10) 17.1700 (10.76) 299.6870 (43.18) 7.8175 (17.30) 178;218 3,286.9082 (0.02) 1321 1 512s test_change_objective_benchmark[optlang-glpk] 296.8780 (45.74) 4,409.9130 (45.65) 322.6875 (45.71) 67.4704 (42.30) 316.7750 (45.64) 9.6910 (21.44) 48;397 3,098.9732 (0.02) 4050 1 512s test_optgp_sample_benchmark 423.5190 (65.26) 936.0930 (9.69) 459.6812 (65.12) 40.0950 (25.14) 450.5270 (64.91) 29.5762 (65.43) 56;43 2,175.4209 (0.02) 931 1 512s test_loopless_benchmark_after 1,330.6910 (205.04) 5,526.6230 (57.21) 1,449.0468 (205.28) 258.4764 (162.05) 1,421.7360 (204.85) 75.0502 (166.04) 7;14 690.1088 (0.00) 287 1 512s test_single_gene_deletion_fba_benchmark[glpk] 5,529.6610 (852.03) 8,062.9140 (83.47) 5,772.0757 (817.70) 230.7742 (144.68) 5,738.8700 (826.87) 167.5640 (370.72) 16;3 173.2479 (0.00) 154 1 512s test_loopless_benchmark_before 7,742.4250 (>1000.0) 11,006.9950 (113.94) 8,704.2344 (>1000.0) 656.0416 (411.30) 8,534.0890 (>1000.0) 459.2325 (>1000.0) 6;4 114.8866 (0.00) 37 1 512s test_minimal_medium_mip_benchmark 8,240.1660 (>1000.0) 8,714.3180 (90.21) 8,435.1621 (>1000.0) 110.0109 (68.97) 8,427.0050 (>1000.0) 142.0143 (314.19) 23;0 118.5514 (0.00) 73 1 512s test_minimal_medium_linear_benchmark 8,283.1620 (>1000.0) 9,736.5380 (100.79) 8,672.1183 (>1000.0) 267.3458 (167.61) 8,603.8220 (>1000.0) 248.8028 (550.45) 11;4 115.3121 (0.00) 67 1 512s test_copy_benchmark[optlang-glpk] 24,022.6970 (>1000.0) 29,539.3170 (305.79) 25,457.6374 (>1000.0) 1,264.8166 (792.97) 25,127.7890 (>1000.0) 1,742.5295 (>1000.0) 13;1 39.2809 (0.00) 39 1 512s test_single_reaction_deletion_benchmark[glpk] 30,180.6060 (>1000.0) 38,289.8410 (396.37) 31,807.6167 (>1000.0) 1,504.8836 (943.48) 32,131.4430 (>1000.0) 1,877.3025 (>1000.0) 4;1 31.4390 (0.00) 31 1 512s test_flux_variability_loopless_benchmark[glpk] 37,285.2820 (>1000.0) 44,987.7790 (465.71) 38,109.0839 (>1000.0) 2,171.5468 (>1000.0) 37,492.5975 (>1000.0) 245.8950 (544.02) 1;1 26.2405 (0.00) 12 1 512s test_deepcopy_benchmark 37,797.0090 (>1000.0) 327,317.0030 (>1000.0) 50,509.4764 (>1000.0) 56,465.1326 (>1000.0) 39,398.0570 (>1000.0) 1,276.1610 (>1000.0) 1;1 19.7983 (0.00) 26 1 512s test_gpr_equality_benchmark 40,056.8390 (>1000.0) 43,914.1280 (454.59) 40,987.0839 (>1000.0) 976.5195 (612.23) 40,640.0030 (>1000.0) 522.2835 (>1000.0) 3;4 24.3979 (0.00) 23 1 512s test_double_reaction_deletion_benchmark 61,564.1780 (>1000.0) 64,930.1660 (672.15) 62,976.8054 (>1000.0) 1,592.0428 (998.13) 62,348.3730 (>1000.0) 2,943.7710 (>1000.0) 1;0 15.8789 (0.00) 5 1 512s test_fastcc_benchmark[glpk] 86,576.0200 (>1000.0) 94,808.7820 (981.45) 90,256.7303 (>1000.0) 2,706.6024 (>1000.0) 90,042.5650 (>1000.0) 3,969.8740 (>1000.0) 5;0 11.0795 (0.00) 11 1 512s test_add_metabolite_benchmark[glpk] 110,632.2140 (>1000.0) 118,442.9160 (>1000.0) 113,572.0101 (>1000.0) 2,340.5425 (>1000.0) 113,524.1320 (>1000.0) 2,826.2520 (>1000.0) 3;1 8.8050 (0.00) 10 1 512s test_add_metabolite_benchmark[cplex] 111,072.4920 (>1000.0) 118,267.9450 (>1000.0) 113,487.1581 (>1000.0) 2,181.5231 (>1000.0) 113,190.4700 (>1000.0) 3,189.0110 (>1000.0) 2;0 8.8116 (0.00) 10 1 512s test_add_metabolite_benchmark[gurobi] 111,437.5650 (>1000.0) 116,857.7090 (>1000.0) 112,938.7357 (>1000.0) 1,745.1833 (>1000.0) 112,266.5640 (>1000.0) 1,863.1303 (>1000.0) 1;1 8.8544 (0.00) 9 1 512s test_achr_init_benchmark 118,439.3320 (>1000.0) 484,145.5090 (>1000.0) 161,975.1311 (>1000.0) 120,862.4954 (>1000.0) 120,802.9970 (>1000.0) 4,926.5050 (>1000.0) 1;1 6.1738 (0.00) 9 1 512s test_optgp_init_benchmark 119,764.6070 (>1000.0) 123,752.8480 (>1000.0) 121,847.0129 (>1000.0) 1,551.8056 (972.90) 121,445.3270 (>1000.0) 2,790.5500 (>1000.0) 4;0 8.2070 (0.00) 8 1 512s test_double_gene_deletion_benchmark 207,664.0750 (>1000.0) 242,186.3320 (>1000.0) 218,270.5640 (>1000.0) 14,603.2869 (>1000.0) 211,091.8650 (>1000.0) 19,143.2348 (>1000.0) 1;0 4.5815 (0.00) 5 1 512s test_single_gene_deletion_linear_moma_benchmark[glpk] 273,800.4440 (>1000.0) 280,783.0230 (>1000.0) 276,220.3062 (>1000.0) 2,918.5378 (>1000.0) 274,616.4790 (>1000.0) 4,040.1535 (>1000.0) 1;0 3.6203 (0.00) 5 1 512s test_gpr_symbolism_benchmark 305,409.1550 (>1000.0) 323,444.9430 (>1000.0) 313,188.3620 (>1000.0) 8,603.7058 (>1000.0) 308,690.0320 (>1000.0) 15,536.9770 (>1000.0) 1;0 3.1930 (0.00) 5 1 512s test_pfba_benchmark[glpk] 365,863.0440 (>1000.0) 380,427.8290 (>1000.0) 371,889.8276 (>1000.0) 6,359.1784 (>1000.0) 369,720.1210 (>1000.0) 10,972.1208 (>1000.0) 1;0 2.6890 (0.00) 5 1 512s test_single_gene_deletion_linear_room_benchmark[glpk] 388,178.2780 (>1000.0) 412,299.8510 (>1000.0) 393,562.4014 (>1000.0) 10,499.5721 (>1000.0) 388,980.3640 (>1000.0) 7,294.5092 (>1000.0) 1;1 2.5409 (0.00) 5 1 512s test_flux_variability_benchmark[glpk] 410,879.4700 (>1000.0) 418,348.1790 (>1000.0) 414,057.9764 (>1000.0) 2,852.7335 (>1000.0) 413,598.6320 (>1000.0) 3,885.1745 (>1000.0) 2;0 2.4151 (0.00) 5 1 512s test_copy_benchmark_large_model[optlang-glpk] 491,496.2570 (>1000.0) 746,450.5520 (>1000.0) 630,803.6904 (>1000.0) 117,109.6382 (>1000.0) 663,090.1770 (>1000.0) 217,436.5823 (>1000.0) 1;0 1.5853 (0.00) 5 1 512s test_geometric_fba_benchmark[glpk] 558,007.2120 (>1000.0) 563,232.8200 (>1000.0) 561,035.7868 (>1000.0) 2,135.5028 (>1000.0) 562,093.5980 (>1000.0) 3,173.1955 (>1000.0) 2;0 1.7824 (0.00) 5 1 512s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 512s 512s Legend: 512s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 512s OPS: Operations Per Second, computed as 1 / Mean 512s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 172 warnings in 142.65s (0:02:22) = 513s Removing patch debian/patches/no_future_dependency.patch 513s Restoring setup.cfg 513s 513s Removing patch debian/patches/32-bit-test.patch 513s Restoring tests/test_io/test_mat.py 513s 513s Removing patch debian/patches/do-not-seek-for-name.patch 513s Restoring src/cobra/io/sbml.py 513s 513s Removing patch debian/patches/ignore_tests.patch 513s Restoring tests/test_io/test_web/test_load.py 513s 513s Removing patch debian/patches/xfail_test_show_versions.patch 513s Restoring tests/test_util/test_util.py 513s 513s Removing patch debian/patches/mathjax.patch 513s Restoring documentation_builder/conf.py 513s 513s No patches applied 513s PASS 514s autopkgtest [04:23:41]: test run-unit-test: -----------------------] 514s run-unit-test PASS 514s autopkgtest [04:23:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 514s autopkgtest [04:23:41]: @@@@@@@@@@@@@@@@@@@@ summary 514s run-unit-test PASS 549s Creating nova instance adt-oracular-ppc64el-python-cobra-20240506-041506-juju-7f2275-prod-proposed-migration-environment-2-a3fccc2e-a66d-4909-86a4-b1d429a8699e from image adt/ubuntu-oracular-ppc64el-server-20240505.img (UUID 5f2b29ba-0f78-4fea-bb4b-40e2e923a051)...