0s autopkgtest [20:18:24]: starting date and time: 2024-05-03 20:18:24+0000 0s autopkgtest [20:18:24]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [20:18:24]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.57dfyhg_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:httpx --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=httpx/0.27.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-4.secgroup --name adt-oracular-ppc64el-python-cobra-20240503-201824-juju-7f2275-prod-proposed-migration-environment-3-5ada6d29-c750-46ef-ba28-49aaea4378e6 --image adt/ubuntu-oracular-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,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/ 514s autopkgtest [20:26:58]: testbed dpkg architecture: ppc64el 514s autopkgtest [20:26:58]: testbed apt version: 2.7.14build2 514s autopkgtest [20:26:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 515s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 515s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 516s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [150 kB] 516s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [2016 kB] 516s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [35.7 kB] 516s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [205 kB] 516s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1260 B] 516s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [1439 kB] 516s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [28.3 kB] 516s Fetched 3943 kB in 1s (2932 kB/s) 516s Reading package lists... 519s Reading package lists... 519s Building dependency tree... 519s Reading state information... 519s Calculating upgrade... 519s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 520s Reading package lists... 520s Building dependency tree... 520s Reading state information... 520s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 520s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 520s Get:2 http://ftpmaster.internal/ubuntu oracular InRelease [64.6 kB] 520s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 521s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 521s Fetched 64.6 kB in 1s (118 kB/s) 522s Reading package lists... 522s Reading package lists... 522s Building dependency tree... 522s Reading state information... 522s Calculating upgrade... 522s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 522s Reading package lists... 522s Building dependency tree... 522s Reading state information... 523s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 525s autopkgtest [20:27:09]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 526s autopkgtest [20:27:10]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 528s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 528s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 528s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 529s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 529s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 529s gpgv: Can't check signature: No public key 529s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 529s autopkgtest [20:27:13]: testing package python-cobra version 0.29.0-1ubuntu2 529s autopkgtest [20:27:13]: build not needed 530s autopkgtest [20:27:14]: test run-unit-test: preparing testbed 531s Reading package lists... 531s Building dependency tree... 531s Reading state information... 532s Starting pkgProblemResolver with broken count: 0 532s Starting 2 pkgProblemResolver with broken count: 0 532s Done 532s The following additional packages will be installed: 532s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 532s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 532s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 532s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 532s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 532s python3-importlib-resources python3-iniconfig python3-more-itertools 532s python3-mpmath python3-numpy python3-optlang python3-packaging 532s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 532s python3-pytest python3-pytest-benchmark python3-pytest-mock 532s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 532s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 532s python3-tabulate python3-zipp quilt swig 532s Suggested packages: 532s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 532s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 532s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 532s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 532s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 532s swig-doc swig-examples 532s Recommended packages: 532s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 532s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 532s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 532s python3-pil isympy-common 532s The following NEW packages will be installed: 532s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 532s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 532s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 532s python3-click python3-cobra python3-colorama python3-cpuinfo 532s python3-dateutil python3-decorator python3-depinfo python3-diskcache 532s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 532s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 532s python3-optlang python3-packaging python3-pandas python3-pandas-lib 532s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 532s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 532s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 532s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 532s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 532s Need to get 52.9 MB/52.9 MB of archives. 532s After this operation, 265 MB of additional disk space will be used. 532s Get:1 /tmp/autopkgtest.pruEGX/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [768 B] 532s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el diffstat ppc64el 1.66-1build1 [33.0 kB] 532s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14-20240412-0ubuntu1 [161 kB] 532s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el gettext ppc64el 0.21-14ubuntu2 [985 kB] 533s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsuitesparseconfig7 ppc64el 1:7.6.1+dfsg-1build1 [12.9 kB] 533s Get:6 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libamd3 ppc64el 1:7.6.1+dfsg-1build1 [36.6 kB] 533s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 533s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libcolamd3 ppc64el 1:7.6.1+dfsg-1build1 [21.6 kB] 533s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14-20240412-0ubuntu1 [574 kB] 533s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el libltdl7 ppc64el 2.4.7-7build1 [48.2 kB] 533s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libglpk40 ppc64el 5.0-1build2 [467 kB] 533s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 533s Get:13 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 533s Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el libpython3.12t64 ppc64el 3.12.3-1 [2553 kB] 533s Get:15 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 534s Get:16 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sniffio all 1.3.0-2 [7216 B] 534s Get:17 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-anyio all 4.2.0-1 [56.5 kB] 534s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 534s Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 534s Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-click all 8.1.6-2 [79.0 kB] 534s Get:21 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-depinfo ppc64el 2.2.0-2 [10.9 kB] 534s Get:22 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-diskcache all 5.4.0-3 [34.6 kB] 534s Get:23 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-h11 all 0.14.0-1 [51.1 kB] 534s Get:24 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-httpcore all 1.0.2-2 [38.3 kB] 534s Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-httpx all 0.27.0-1 [60.9 kB] 534s Get:26 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-more-itertools all 10.2.0-1 [52.9 kB] 534s Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-zipp all 1.0.0-6 [6090 B] 534s Get:28 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-importlib-resources all 6.0.1-1 [22.1 kB] 534s Get:29 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-6ubuntu1 [4446 kB] 534s Get:30 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-swiglpk ppc64el 5.0.10-1build1 [85.0 kB] 534s Get:31 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-mpmath all 1.2.1-3 [421 kB] 534s Get:32 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sympy all 1.12-7 [3966 kB] 534s Get:33 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-optlang all 1.8.1-1 [82.7 kB] 534s Get:34 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 534s Get:35 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-7 [4602 kB] 535s Get:36 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pandas all 2.1.4+dfsg-7 [3042 kB] 535s Get:37 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-pydantic ppc64el 1.10.14-1 [1825 kB] 535s Get:38 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-ruamel.yaml.clib ppc64el 0.2.8-1build1 [159 kB] 535s Get:39 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 535s Get:40 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-simplejson ppc64el 3.19.2-1build2 [60.6 kB] 535s Get:41 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-tabulate all 0.8.10-1 [38.2 kB] 535s Get:42 http://ftpmaster.internal/ubuntu oracular/universe ppc64el swig ppc64el 4.2.0-2ubuntu1 [1261 kB] 535s Get:43 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-sbml5 ppc64el 5.20.2+dfsg-3 [3752 kB] 535s Get:44 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cobra ppc64el 0.29.0-1ubuntu2 [1119 kB] 535s Get:45 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cpuinfo all 9.0.0-1 [21.2 kB] 535s Get:46 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 535s Get:47 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 535s Get:48 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.0-1 [41.1 kB] 535s Get:49 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB] 535s Get:50 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 535s Get:51 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 535s Get:52 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 535s Get:53 http://ftpmaster.internal/ubuntu oracular/universe ppc64el quilt all 0.67+really0.67-4 [436 kB] 535s Get:54 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-scipy ppc64el 1.11.4-6build1 [17.0 MB] 536s Fetched 52.9 MB in 4s (14.0 MB/s) 536s Selecting previously unselected package diffstat. 536s (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 ... 72135 files and directories currently installed.) 536s Preparing to unpack .../00-diffstat_1.66-1build1_ppc64el.deb ... 536s Unpacking diffstat (1.66-1build1) ... 536s Selecting previously unselected package libgomp1:ppc64el. 536s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_ppc64el.deb ... 536s Unpacking libgomp1:ppc64el (14-20240412-0ubuntu1) ... 536s Selecting previously unselected package gettext. 536s Preparing to unpack .../02-gettext_0.21-14ubuntu2_ppc64el.deb ... 536s Unpacking gettext (0.21-14ubuntu2) ... 536s Selecting previously unselected package libsuitesparseconfig7:ppc64el. 536s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 536s Unpacking libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1build1) ... 536s Selecting previously unselected package libamd3:ppc64el. 536s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 536s Unpacking libamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 536s Selecting previously unselected package libblas3:ppc64el. 536s Preparing to unpack .../05-libblas3_3.12.0-3build1_ppc64el.deb ... 536s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 536s Selecting previously unselected package libcolamd3:ppc64el. 536s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_ppc64el.deb ... 536s Unpacking libcolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 536s Selecting previously unselected package libgfortran5:ppc64el. 536s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_ppc64el.deb ... 536s Unpacking libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 536s Selecting previously unselected package libltdl7:ppc64el. 536s Preparing to unpack .../08-libltdl7_2.4.7-7build1_ppc64el.deb ... 536s Unpacking libltdl7:ppc64el (2.4.7-7build1) ... 536s Selecting previously unselected package libglpk40:ppc64el. 536s Preparing to unpack .../09-libglpk40_5.0-1build2_ppc64el.deb ... 536s Unpacking libglpk40:ppc64el (5.0-1build2) ... 536s Selecting previously unselected package liblapack3:ppc64el. 536s Preparing to unpack .../10-liblapack3_3.12.0-3build1_ppc64el.deb ... 536s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 536s Selecting previously unselected package liblbfgsb0:ppc64el. 536s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 536s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 536s Selecting previously unselected package libpython3.12t64:ppc64el. 536s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_ppc64el.deb ... 536s Unpacking libpython3.12t64:ppc64el (3.12.3-1) ... 536s Selecting previously unselected package python-cobra-data. 536s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 536s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 537s Selecting previously unselected package python3-sniffio. 537s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 537s Unpacking python3-sniffio (1.3.0-2) ... 537s Selecting previously unselected package python3-anyio. 537s Preparing to unpack .../15-python3-anyio_4.2.0-1_all.deb ... 537s Unpacking python3-anyio (4.2.0-1) ... 537s Selecting previously unselected package python3-appdirs. 537s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 537s Unpacking python3-appdirs (1.4.4-4) ... 537s Selecting previously unselected package python3-colorama. 537s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 537s Unpacking python3-colorama (0.4.6-4) ... 537s Selecting previously unselected package python3-click. 537s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 537s Unpacking python3-click (8.1.6-2) ... 537s Selecting previously unselected package python3-depinfo. 537s Preparing to unpack .../19-python3-depinfo_2.2.0-2_ppc64el.deb ... 537s Unpacking python3-depinfo (2.2.0-2) ... 537s Selecting previously unselected package python3-diskcache. 537s Preparing to unpack .../20-python3-diskcache_5.4.0-3_all.deb ... 537s Unpacking python3-diskcache (5.4.0-3) ... 537s Selecting previously unselected package python3-h11. 537s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 537s Unpacking python3-h11 (0.14.0-1) ... 537s Selecting previously unselected package python3-httpcore. 537s Preparing to unpack .../22-python3-httpcore_1.0.2-2_all.deb ... 537s Unpacking python3-httpcore (1.0.2-2) ... 537s Selecting previously unselected package python3-httpx. 537s Preparing to unpack .../23-python3-httpx_0.27.0-1_all.deb ... 537s Unpacking python3-httpx (0.27.0-1) ... 537s Selecting previously unselected package python3-more-itertools. 537s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 537s Unpacking python3-more-itertools (10.2.0-1) ... 537s Selecting previously unselected package python3-zipp. 537s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 537s Unpacking python3-zipp (1.0.0-6) ... 537s Selecting previously unselected package python3-importlib-resources. 537s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 537s Unpacking python3-importlib-resources (6.0.1-1) ... 537s Selecting previously unselected package python3-numpy. 537s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_ppc64el.deb ... 537s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 537s Selecting previously unselected package python3-swiglpk. 537s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_ppc64el.deb ... 537s Unpacking python3-swiglpk (5.0.10-1build1) ... 537s Selecting previously unselected package python3-mpmath. 537s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 537s Unpacking python3-mpmath (1.2.1-3) ... 537s Selecting previously unselected package python3-sympy. 537s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 537s Unpacking python3-sympy (1.12-7) ... 537s Selecting previously unselected package python3-optlang. 537s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 537s Unpacking python3-optlang (1.8.1-1) ... 537s Selecting previously unselected package python3-dateutil. 537s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 537s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 538s Selecting previously unselected package python3-pandas-lib:ppc64el. 538s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_ppc64el.deb ... 538s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-7) ... 538s Selecting previously unselected package python3-pandas. 538s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 538s Unpacking python3-pandas (2.1.4+dfsg-7) ... 538s Selecting previously unselected package python3-pydantic. 538s Preparing to unpack .../35-python3-pydantic_1.10.14-1_ppc64el.deb ... 538s Unpacking python3-pydantic (1.10.14-1) ... 538s Selecting previously unselected package python3-ruamel.yaml.clib:ppc64el. 538s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8-1build1_ppc64el.deb ... 538s Unpacking python3-ruamel.yaml.clib:ppc64el (0.2.8-1build1) ... 538s Selecting previously unselected package python3-ruamel.yaml. 538s Preparing to unpack .../37-python3-ruamel.yaml_0.17.21-1_all.deb ... 538s Unpacking python3-ruamel.yaml (0.17.21-1) ... 538s Selecting previously unselected package python3-simplejson. 538s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_ppc64el.deb ... 538s Unpacking python3-simplejson (3.19.2-1build2) ... 538s Selecting previously unselected package python3-tabulate. 538s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 538s Unpacking python3-tabulate (0.8.10-1) ... 538s Selecting previously unselected package swig. 538s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_ppc64el.deb ... 538s Unpacking swig (4.2.0-2ubuntu1) ... 538s Selecting previously unselected package python3-sbml5. 538s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_ppc64el.deb ... 538s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 539s Selecting previously unselected package python3-cobra. 539s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_ppc64el.deb ... 539s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 539s Selecting previously unselected package python3-cpuinfo. 539s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 539s Unpacking python3-cpuinfo (9.0.0-1) ... 539s Selecting previously unselected package python3-decorator. 539s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 539s Unpacking python3-decorator (5.1.1-5) ... 539s Selecting previously unselected package python3-iniconfig. 539s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 539s Unpacking python3-iniconfig (1.1.1-2) ... 539s Selecting previously unselected package python3-packaging. 539s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 539s Unpacking python3-packaging (24.0-1) ... 539s Selecting previously unselected package python3-pluggy. 539s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 539s Unpacking python3-pluggy (1.4.0-1) ... 539s Selecting previously unselected package python3-pytest. 539s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 539s Unpacking python3-pytest (7.4.4-1) ... 539s Selecting previously unselected package python3-pytest-benchmark. 539s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 539s Unpacking python3-pytest-benchmark (4.0.0-3) ... 539s Selecting previously unselected package python3-pytest-mock. 539s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 539s Unpacking python3-pytest-mock (3.12.0-1.1) ... 539s Selecting previously unselected package quilt. 539s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 539s Unpacking quilt (0.67+really0.67-4) ... 539s Selecting previously unselected package python3-scipy. 539s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_ppc64el.deb ... 539s Unpacking python3-scipy (1.11.4-6build1) ... 539s Selecting previously unselected package autopkgtest-satdep. 539s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 539s Unpacking autopkgtest-satdep (0) ... 539s Setting up python3-more-itertools (10.2.0-1) ... 540s Setting up python3-iniconfig (1.1.1-2) ... 540s Setting up python3-sniffio (1.3.0-2) ... 540s Setting up swig (4.2.0-2ubuntu1) ... 540s Setting up python3-anyio (4.2.0-1) ... 540s Setting up python3-colorama (0.4.6-4) ... 540s Setting up python3-ruamel.yaml.clib:ppc64el (0.2.8-1build1) ... 540s Setting up python3-tabulate (0.8.10-1) ... 540s Setting up python3-zipp (1.0.0-6) ... 541s Setting up libgomp1:ppc64el (14-20240412-0ubuntu1) ... 541s Setting up python3-click (8.1.6-2) ... 541s Setting up libpython3.12t64:ppc64el (3.12.3-1) ... 541s Setting up python3-simplejson (3.19.2-1build2) ... 541s Setting up python3-decorator (5.1.1-5) ... 541s Setting up libblas3:ppc64el (3.12.0-3build1) ... 541s 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 541s Setting up python3-packaging (24.0-1) ... 541s Setting up python3-pydantic (1.10.14-1) ... 542s Setting up diffstat (1.66-1build1) ... 542s Setting up python3-h11 (0.14.0-1) ... 542s Setting up python3-depinfo (2.2.0-2) ... 542s Setting up python3-cpuinfo (9.0.0-1) ... 542s Setting up libltdl7:ppc64el (2.4.7-7build1) ... 542s Setting up libgfortran5:ppc64el (14-20240412-0ubuntu1) ... 542s Setting up python3-pluggy (1.4.0-1) ... 542s Setting up python3-ruamel.yaml (0.17.21-1) ... 542s Setting up libsuitesparseconfig7:ppc64el (1:7.6.1+dfsg-1build1) ... 542s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 543s Setting up python3-mpmath (1.2.1-3) ... 543s Setting up python3-diskcache (5.4.0-3) ... 543s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 543s Setting up python3-appdirs (1.4.4-4) ... 544s Setting up python3-httpcore (1.0.2-2) ... 544s Setting up python3-sympy (1.12-7) ... 551s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 551s 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 551s Setting up gettext (0.21-14ubuntu2) ... 551s Setting up libamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 551s Setting up python3-importlib-resources (6.0.1-1) ... 551s Setting up libcolamd3:ppc64el (1:7.6.1+dfsg-1build1) ... 551s Setting up python3-pytest (7.4.4-1) ... 551s Setting up quilt (0.67+really0.67-4) ... 551s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 552s Setting up python3-httpx (0.27.0-1) ... 552s Setting up libglpk40:ppc64el (5.0-1build2) ... 552s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 554s Setting up python3-pytest-mock (3.12.0-1.1) ... 555s Setting up python3-swiglpk (5.0.10-1build1) ... 555s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 555s Setting up python3-optlang (1.8.1-1) ... 555s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 555s """A representation of the convex optimizatgion problem in standard form. 555s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 555s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 555s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 555s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 555s Setting up python3-pytest-benchmark (4.0.0-3) ... 555s Setting up python3-scipy (1.11.4-6build1) ... 559s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-7) ... 559s Setting up python3-pandas (2.1.4+dfsg-7) ... 565s Setting up python3-cobra (0.29.0-1ubuntu2) ... 565s Setting up autopkgtest-satdep (0) ... 565s Processing triggers for man-db (2.12.0-4build2) ... 565s Processing triggers for install-info (7.1-3build2) ... 565s Processing triggers for libc-bin (2.39-0ubuntu8) ... 569s (Reading database ... 80145 files and directories currently installed.) 569s Removing autopkgtest-satdep (0) ... 569s autopkgtest [20:27:53]: test run-unit-test: [----------------------- 570s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 570s Running Tests 570s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 573s ============================= test session starts ============================== 573s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 573s 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) 573s rootdir: /tmp/autopkgtest.pruEGX/autopkgtest_tmp 573s plugins: mock-3.12.0, benchmark-4.0.0, anyio-4.2.0 573s collected 551 items 573s 573s tests/test_core/test_configuration.py ...... [ 1%] 579s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 580s ...................x....... [ 12%] 580s tests/test_core/test_dictlist.py ...................... [ 16%] 580s tests/test_core/test_formula.py ..... [ 17%] 580s tests/test_core/test_gene.py . [ 17%] 581s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 593s .......................... [ 29%] 593s tests/test_core/test_group.py .. [ 30%] 593s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 603s tests/test_core/test_model.py .......................................... [ 39%] 604s ...........s..s.ss. [ 43%] 604s tests/test_core/test_solution.py .ss [ 43%] 611s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 613s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 617s tests/test_flux_analysis/test_geometric.py .. [ 46%] 618s tests/test_flux_analysis/test_moma.py . [ 46%] 622s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 623s tests/test_flux_analysis/test_reaction.py . [ 47%] 626s tests/test_flux_analysis/test_room.py .... [ 47%] 631s tests/test_flux_analysis/test_variability.py ....... [ 49%] 631s tests/test_flux_analysis/test_deletion.py sss [ 49%] 631s tests/test_flux_analysis/test_moma.py s [ 49%] 635s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 639s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 639s tests/test_flux_analysis/test_helpers.py ... [ 51%] 640s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 643s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 644s tests/test_flux_analysis/test_variability.py ....... [ 54%] 644s tests/test_io/test_annotation.py .. [ 55%] 644s tests/test_io/test_annotation_format.py .. [ 55%] 648s tests/test_io/test_io_order.py ........................... [ 60%] 648s tests/test_io/test_json.py .... [ 61%] 671s tests/test_io/test_mat.py ............... [ 64%] 671s tests/test_io/test_notes.py . [ 64%] 671s tests/test_io/test_pickle.py .. [ 64%] 680s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 680s tests/test_io/test_yaml.py .x [ 72%] 681s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 681s tests/test_manipulation/test_annotate.py . [ 73%] 682s tests/test_manipulation/test_delete.py ....... [ 75%] 682s tests/test_manipulation/test_modify.py ... [ 75%] 682s tests/test_manipulation/test_validate.py .. [ 76%] 682s tests/test_medium/test_boundary_types.py ......... [ 77%] 684s tests/test_medium/test_minimal_medium.py .......... [ 79%] 687s tests/test_sampling/test_achr.py ...... [ 80%] 690s tests/test_sampling/test_optgp.py ...... [ 81%] 697s tests/test_sampling/test_sampling.py .......... [ 83%] 699s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 701s tests/test_summary/test_model_summary.py ............... [ 89%] 703s tests/test_summary/test_reaction_summary.py .................... [ 92%] 703s tests/test_util/test_array.py .. [ 93%] 703s tests/test_util/test_context.py ... [ 93%] 703s tests/test_util/test_process_pool.py ............... [ 96%] 705s tests/test_util/test_solver.py ..............s [ 99%] 705s tests/test_util/test_util.py ...X [100%] 705s 705s =============================== warnings summary =============================== 705s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 705s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 705s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 705s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 705s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 705s /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)'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 705s warn( 705s 705s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 705s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 705s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 705s warn( 705s 705s tests/test_core/test_model.py::test_reaction_delete 705s tests/test_core/test_model.py::test_reaction_delete 705s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 705s warn( 705s 705s tests/test_core/test_model.py::test_group_loss_of_elements 705s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 705s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 705s warn("need to pass in a list") 705s 705s tests/test_core/test_model.py::test_change_objective 705s tests/test_core/test_model.py::test_change_objective 705s tests/test_core/test_model.py::test_change_objective 705s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 705s warn("Please use reaction.flux instead.", DeprecationWarning) 705s 705s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 705s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 705s /tmp/autopkgtest.pruEGX/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 705s assert math.isnan(sol.growth) 705s 705s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 705s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 705s /tmp/autopkgtest.pruEGX/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 705s assert math.isnan(sol_one.growth) 705s 705s tests/test_io/test_json.py: 1 warning 705s tests/test_io/test_mat.py: 5 warnings 705s tests/test_io/test_pickle.py: 1 warning 705s tests/test_io/test_sbml.py: 9 warnings 705s tests/test_io/test_yaml.py: 1 warning 705s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 705s warn(f"Solver status is '{status}'.", UserWarning) 705s 705s tests/test_medium/test_boundary_types.py: 96 warnings 705s /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]` 705s return most[0] 705s 705s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 705s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 705s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 705s /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]` 705s compartment = most[matches[most]][0] 705s 705s tests/test_util/test_process_pool.py::test_with_context 705s /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 705s self._pool.__enter__() 705s 705s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 705s 705s -------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests --------------------------------------------------------------------------------------------------------------------- 705s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 705s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 705s test_subtract_metabolite_benchmark[glpk] 6.4830 (1.0) 72.8800 (2.93) 6.7991 (1.0) 1.0824 (1.77) 6.7550 (1.0) 0.0910 (1.0) 21;100 147,078.8025 (1.0) 4666 1 705s test_subtract_metabolite_benchmark[gurobi] 6.5630 (1.01) 126.7490 (5.10) 6.8916 (1.01) 1.8530 (3.02) 6.8300 (1.01) 0.1000 (1.10) 19;96 145,104.1285 (0.99) 4709 1 705s test_subtract_metabolite_benchmark[cplex] 6.6090 (1.02) 24.8620 (1.0) 6.9101 (1.02) 0.6131 (1.0) 6.8660 (1.02) 0.1010 (1.11) 34;119 144,716.2168 (0.98) 4563 1 705s test_achr_sample_benchmark 261.6670 (40.36) 346.7590 (13.95) 267.0113 (39.27) 4.9508 (8.08) 265.6360 (39.32) 1.4605 (16.05) 194;242 3,745.1600 (0.03) 1545 1 705s test_change_objective_benchmark[optlang-glpk] 284.3300 (43.86) 858.3900 (34.53) 296.6259 (43.63) 13.9242 (22.71) 295.5395 (43.75) 7.8025 (85.74) 342;375 3,371.2503 (0.02) 4512 1 705s test_optgp_sample_benchmark 400.5420 (61.78) 548.1730 (22.05) 416.6577 (61.28) 12.8175 (20.91) 414.1570 (61.31) 7.5970 (83.48) 412;145 2,400.0517 (0.02) 1590 1 705s test_loopless_benchmark_after 1,339.3220 (206.59) 1,758.5620 (70.73) 1,361.7601 (200.29) 39.9284 (65.13) 1,353.9430 (200.44) 19.1440 (210.37) 9;11 734.3438 (0.00) 322 1 705s test_single_gene_deletion_fba_benchmark[glpk] 5,231.6840 (806.99) 6,267.8780 (252.11) 5,428.3130 (798.39) 158.5888 (258.68) 5,467.5070 (809.40) 242.1000 (>1000.0) 39;2 184.2193 (0.00) 156 1 705s test_minimal_medium_linear_benchmark 7,326.0560 (>1000.0) 9,491.4630 (381.77) 7,588.9037 (>1000.0) 284.9335 (464.76) 7,522.5460 (>1000.0) 44.1260 (484.90) 3;10 131.7713 (0.00) 79 1 705s test_minimal_medium_mip_benchmark 7,379.8970 (>1000.0) 7,917.8310 (318.47) 7,511.6309 (>1000.0) 117.2755 (191.29) 7,461.9440 (>1000.0) 93.3563 (>1000.0) 15;12 133.1269 (0.00) 79 1 705s test_loopless_benchmark_before 7,516.0900 (>1000.0) 10,491.0160 (421.97) 7,667.3276 (>1000.0) 348.0288 (567.68) 7,599.0330 (>1000.0) 105.4260 (>1000.0) 2;8 130.4235 (0.00) 76 1 705s test_copy_benchmark[optlang-glpk] 23,368.3150 (>1000.0) 25,433.4920 (>1000.0) 24,390.4753 (>1000.0) 558.2699 (910.61) 24,243.0120 (>1000.0) 992.8320 (>1000.0) 16;0 40.9996 (0.00) 42 1 705s test_single_reaction_deletion_benchmark[glpk] 29,150.8020 (>1000.0) 31,695.1170 (>1000.0) 30,210.5487 (>1000.0) 622.5280 (>1000.0) 30,081.0150 (>1000.0) 778.6185 (>1000.0) 10;0 33.1010 (0.00) 33 1 705s test_flux_variability_loopless_benchmark[glpk] 31,971.4850 (>1000.0) 39,486.3010 (>1000.0) 32,846.0821 (>1000.0) 1,971.6826 (>1000.0) 32,225.3975 (>1000.0) 294.4290 (>1000.0) 1;2 30.4450 (0.00) 14 1 705s test_deepcopy_benchmark 36,168.9570 (>1000.0) 277,440.1310 (>1000.0) 45,927.7635 (>1000.0) 45,377.9259 (>1000.0) 37,297.6825 (>1000.0) 878.9045 (>1000.0) 1;2 21.7733 (0.00) 28 1 705s test_gpr_equality_benchmark 39,210.3350 (>1000.0) 41,045.5980 (>1000.0) 39,885.6575 (>1000.0) 471.7566 (769.49) 39,760.7370 (>1000.0) 720.4320 (>1000.0) 6;0 25.0717 (0.00) 23 1 705s test_double_reaction_deletion_benchmark 59,960.0010 (>1000.0) 60,169.9810 (>1000.0) 60,050.4168 (>1000.0) 88.5173 (144.38) 60,009.7540 (>1000.0) 142.1875 (>1000.0) 2;0 16.6527 (0.00) 5 1 705s test_fastcc_benchmark[glpk] 83,926.0410 (>1000.0) 193,587.8580 (>1000.0) 94,306.2880 (>1000.0) 31,276.0860 (>1000.0) 85,561.9610 (>1000.0) 1,497.8605 (>1000.0) 1;1 10.6037 (0.00) 12 1 705s test_add_metabolite_benchmark[glpk] 109,816.9860 (>1000.0) 112,427.8570 (>1000.0) 110,536.6357 (>1000.0) 829.2538 (>1000.0) 110,134.9410 (>1000.0) 903.2262 (>1000.0) 1;1 9.0468 (0.00) 9 1 705s test_add_metabolite_benchmark[cplex] 109,880.2610 (>1000.0) 111,738.0410 (>1000.0) 110,630.6405 (>1000.0) 474.0693 (773.26) 110,583.9870 (>1000.0) 319.7990 (>1000.0) 2;2 9.0391 (0.00) 10 1 705s test_add_metabolite_benchmark[gurobi] 110,771.9350 (>1000.0) 112,335.1170 (>1000.0) 111,563.4354 (>1000.0) 425.1718 (693.51) 111,530.0525 (>1000.0) 510.1530 (>1000.0) 2;0 8.9635 (0.00) 10 1 705s test_achr_init_benchmark 113,853.2270 (>1000.0) 117,052.0360 (>1000.0) 115,437.0983 (>1000.0) 1,147.1424 (>1000.0) 115,460.4920 (>1000.0) 1,999.1860 (>1000.0) 4;0 8.6627 (0.00) 9 1 705s test_optgp_init_benchmark 115,399.4340 (>1000.0) 117,917.0140 (>1000.0) 116,455.3523 (>1000.0) 1,009.2129 (>1000.0) 116,597.4220 (>1000.0) 1,735.3275 (>1000.0) 3;0 8.5870 (0.00) 9 1 705s test_double_gene_deletion_benchmark 200,955.3780 (>1000.0) 237,829.8110 (>1000.0) 215,659.5266 (>1000.0) 16,756.9283 (>1000.0) 208,230.4790 (>1000.0) 29,350.3085 (>1000.0) 1;0 4.6369 (0.00) 5 1 705s test_single_gene_deletion_linear_moma_benchmark[glpk] 260,829.0250 (>1000.0) 616,885.9440 (>1000.0) 332,568.1070 (>1000.0) 158,939.6858 (>1000.0) 261,547.3490 (>1000.0) 90,012.2120 (>1000.0) 1;1 3.0069 (0.00) 5 1 705s test_gpr_symbolism_benchmark 297,915.1440 (>1000.0) 304,158.4010 (>1000.0) 301,311.5760 (>1000.0) 2,223.3753 (>1000.0) 301,561.7940 (>1000.0) 1,731.8450 (>1000.0) 2;0 3.3188 (0.00) 5 1 705s test_pfba_benchmark[glpk] 360,909.5010 (>1000.0) 492,981.0990 (>1000.0) 388,688.8752 (>1000.0) 58,320.4019 (>1000.0) 363,806.3220 (>1000.0) 35,275.4700 (>1000.0) 1;1 2.5728 (0.00) 5 1 705s test_single_gene_deletion_linear_room_benchmark[glpk] 376,948.7880 (>1000.0) 384,452.3240 (>1000.0) 381,645.6352 (>1000.0) 3,034.8006 (>1000.0) 382,785.0170 (>1000.0) 4,322.8062 (>1000.0) 1;0 2.6202 (0.00) 5 1 705s test_flux_variability_benchmark[glpk] 392,585.9800 (>1000.0) 397,900.0040 (>1000.0) 394,686.1232 (>1000.0) 1,977.8126 (>1000.0) 394,550.2440 (>1000.0) 2,008.3000 (>1000.0) 2;0 2.5337 (0.00) 5 1 705s test_copy_benchmark_large_model[optlang-glpk] 484,751.8520 (>1000.0) 730,699.0320 (>1000.0) 573,038.9306 (>1000.0) 121,138.7757 (>1000.0) 486,438.5570 (>1000.0) 205,358.1460 (>1000.0) 1;0 1.7451 (0.00) 5 1 705s test_geometric_fba_benchmark[glpk] 524,148.9250 (>1000.0) 538,381.8780 (>1000.0) 531,164.2192 (>1000.0) 5,684.1202 (>1000.0) 529,672.5260 (>1000.0) 8,847.9035 (>1000.0) 2;0 1.8827 (0.00) 5 1 705s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 705s 705s Legend: 705s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 705s OPS: Operations Per Second, computed as 1 / Mean 705s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 171 warnings in 133.42s (0:02:13) = 706s Removing patch debian/patches/no_future_dependency.patch 706s Restoring setup.cfg 706s 706s Removing patch debian/patches/32-bit-test.patch 706s Restoring tests/test_io/test_mat.py 706s 706s Removing patch debian/patches/do-not-seek-for-name.patch 706s Restoring src/cobra/io/sbml.py 706s 706s Removing patch debian/patches/ignore_tests.patch 706s Restoring tests/test_io/test_web/test_load.py 706s 706s Removing patch debian/patches/xfail_test_show_versions.patch 706s Restoring tests/test_util/test_util.py 706s 706s Removing patch debian/patches/mathjax.patch 706s Restoring documentation_builder/conf.py 706s 706s No patches applied 706s PASS 706s autopkgtest [20:30:10]: test run-unit-test: -----------------------] 707s autopkgtest [20:30:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 707s run-unit-test PASS 707s autopkgtest [20:30:11]: @@@@@@@@@@@@@@@@@@@@ summary 707s run-unit-test PASS 745s Creating nova instance adt-oracular-ppc64el-python-cobra-20240503-201824-juju-7f2275-prod-proposed-migration-environment-3-5ada6d29-c750-46ef-ba28-49aaea4378e6 from image adt/ubuntu-oracular-ppc64el-server-20240503.img (UUID 60999710-d97e-47d3-8cca-85ddcf19ebc0)...