0s autopkgtest [22:29:11]: starting date and time: 2024-05-11 22:29:11+0000 0s autopkgtest [22:29:11]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [22:29:11]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fl0agpx_/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.108 lxd-armhf-10.145.243.108:autopkgtest/ubuntu/oracular/armhf 31s autopkgtest [22:29:42]: testbed dpkg architecture: armhf 32s autopkgtest [22:29:43]: testbed apt version: 2.7.14build2 32s autopkgtest [22:29:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 40s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [121 kB] 40s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 40s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [16.8 kB] 40s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1169 kB] 40s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [170 kB] 40s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [970 kB] 40s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [19.2 kB] 41s Fetched 2542 kB in 1s (2441 kB/s) 41s Reading package lists... 57s tee: /proc/self/fd/2: Permission denied 79s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 81s Reading package lists... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s autopkgtest [22:30:37]: rebooting testbed after setup commands that affected boot 127s autopkgtest [22:31:18]: testbed running kernel: Linux 5.15.0-106-generic #116-Ubuntu SMP Wed Apr 17 09:19:22 UTC 2024 154s autopkgtest [22:31:45]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 172s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 172s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 172s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 173s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 173s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 173s gpgv: Can't check signature: No public key 173s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 173s autopkgtest [22:32:04]: testing package python-cobra version 0.29.0-1ubuntu2 175s autopkgtest [22:32:06]: build not needed 178s autopkgtest [22:32:09]: test run-unit-test: preparing testbed 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 192s The following additional packages will be installed: 192s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 192s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 192s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 192s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 192s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 192s python3-importlib-resources python3-iniconfig python3-more-itertools 192s python3-mpmath python3-numpy python3-optlang python3-packaging 192s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 192s python3-pytest python3-pytest-benchmark python3-pytest-mock 192s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 192s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 192s python3-tabulate python3-zipp quilt swig 192s Suggested packages: 192s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 192s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 192s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 192s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 192s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 192s swig-doc swig-examples 192s Recommended packages: 192s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 192s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 192s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 192s python3-pil isympy-common 192s The following NEW packages will be installed: 192s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 192s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 192s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 192s python3-click python3-cobra python3-colorama python3-cpuinfo 192s python3-dateutil python3-decorator python3-depinfo python3-diskcache 192s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 192s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 192s python3-optlang python3-packaging python3-pandas python3-pandas-lib 192s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 192s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 192s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 192s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 192s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 47.5 MB/47.5 MB of archives. 192s After this operation, 195 MB of additional disk space will be used. 192s Get:1 /tmp/autopkgtest.htB337/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [764 B] 192s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf diffstat armhf 1.66-1build1 [27.7 kB] 192s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libgomp1 armhf 14-20240412-0ubuntu1 [125 kB] 192s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf gettext armhf 0.21-14ubuntu2 [800 kB] 193s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libsuitesparseconfig7 armhf 1:7.6.1+dfsg-1build1 [12.1 kB] 193s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libamd3 armhf 1:7.6.1+dfsg-1build1 [28.2 kB] 193s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 193s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf libcolamd3 armhf 1:7.6.1+dfsg-1build1 [20.1 kB] 193s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14-20240412-0ubuntu1 [316 kB] 193s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf libltdl7 armhf 2.4.7-7build1 [37.6 kB] 193s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 193s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 194s Get:13 http://ftpmaster.internal/ubuntu oracular/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 194s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf libpython3.12t64 armhf 3.12.3-1 [2058 kB] 194s Get:15 http://ftpmaster.internal/ubuntu oracular/universe armhf python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 194s Get:16 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sniffio all 1.3.0-2 [7216 B] 194s Get:17 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-anyio all 4.3.0-1 [56.6 kB] 194s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 194s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 194s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.6-2 [79.0 kB] 194s Get:21 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-depinfo armhf 2.2.0-2 [10.9 kB] 194s Get:22 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-diskcache all 5.6.3-1 [35.1 kB] 194s Get:23 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-h11 all 0.14.0-1 [51.1 kB] 194s Get:24 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-httpcore all 1.0.4-1 [38.8 kB] 194s Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-httpx all 0.27.0-1 [60.9 kB] 194s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf python3-more-itertools all 10.2.0-1 [52.9 kB] 194s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf python3-zipp all 1.0.0-6 [6090 B] 194s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf python3-importlib-resources all 6.0.1-1 [22.1 kB] 194s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-6ubuntu1 [3541 kB] 195s Get:30 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-swiglpk armhf 5.0.10-1build1 [66.3 kB] 195s Get:31 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 195s Get:32 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sympy all 1.12-7 [3966 kB] 197s Get:33 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-optlang all 1.8.1-1 [82.7 kB] 197s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 197s Get:35 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pandas-lib armhf 2.1.4+dfsg-7 [4462 kB] 197s Get:36 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pandas all 2.1.4+dfsg-7 [3042 kB] 197s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf python3-pydantic armhf 1.10.14-1 [1738 kB] 197s Get:38 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-ruamel.yaml.clib armhf 0.2.8-1build1 [120 kB] 197s Get:39 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 197s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf python3-simplejson armhf 3.19.2-1build2 [52.0 kB] 197s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf python3-tabulate all 0.8.10-1 [38.2 kB] 197s Get:42 http://ftpmaster.internal/ubuntu oracular/universe armhf swig armhf 4.2.0-2ubuntu1 [1115 kB] 197s Get:43 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sbml5 armhf 5.20.2+dfsg-3 [3497 kB] 197s Get:44 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cobra armhf 0.29.0-1ubuntu2 [1119 kB] 197s Get:45 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cpuinfo all 9.0.0+git20221119-1 [21.4 kB] 197s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 197s Get:47 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 197s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.0-1 [41.1 kB] 197s Get:49 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.4.0-1 [20.4 kB] 197s Get:50 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest all 7.4.4-1 [305 kB] 197s Get:51 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 197s Get:52 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 197s Get:53 http://ftpmaster.internal/ubuntu oracular/universe armhf quilt all 0.67+really0.67-4 [436 kB] 197s Get:54 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-scipy armhf 1.11.4-6build1 [15.1 MB] 198s Fetched 47.5 MB in 5s (9605 kB/s) 198s Selecting previously unselected package diffstat. 198s (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 ... 57881 files and directories currently installed.) 198s Preparing to unpack .../00-diffstat_1.66-1build1_armhf.deb ... 198s Unpacking diffstat (1.66-1build1) ... 198s Selecting previously unselected package libgomp1:armhf. 198s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_armhf.deb ... 198s Unpacking libgomp1:armhf (14-20240412-0ubuntu1) ... 198s Selecting previously unselected package gettext. 198s Preparing to unpack .../02-gettext_0.21-14ubuntu2_armhf.deb ... 198s Unpacking gettext (0.21-14ubuntu2) ... 198s Selecting previously unselected package libsuitesparseconfig7:armhf. 198s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_armhf.deb ... 198s Unpacking libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1build1) ... 198s Selecting previously unselected package libamd3:armhf. 198s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_armhf.deb ... 198s Unpacking libamd3:armhf (1:7.6.1+dfsg-1build1) ... 198s Selecting previously unselected package libblas3:armhf. 198s Preparing to unpack .../05-libblas3_3.12.0-3build1_armhf.deb ... 198s Unpacking libblas3:armhf (3.12.0-3build1) ... 198s Selecting previously unselected package libcolamd3:armhf. 198s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_armhf.deb ... 198s Unpacking libcolamd3:armhf (1:7.6.1+dfsg-1build1) ... 198s Selecting previously unselected package libgfortran5:armhf. 198s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_armhf.deb ... 198s Unpacking libgfortran5:armhf (14-20240412-0ubuntu1) ... 198s Selecting previously unselected package libltdl7:armhf. 198s Preparing to unpack .../08-libltdl7_2.4.7-7build1_armhf.deb ... 198s Unpacking libltdl7:armhf (2.4.7-7build1) ... 198s Selecting previously unselected package libglpk40:armhf. 198s Preparing to unpack .../09-libglpk40_5.0-1build2_armhf.deb ... 198s Unpacking libglpk40:armhf (5.0-1build2) ... 198s Selecting previously unselected package liblapack3:armhf. 198s Preparing to unpack .../10-liblapack3_3.12.0-3build1_armhf.deb ... 198s Unpacking liblapack3:armhf (3.12.0-3build1) ... 198s Selecting previously unselected package liblbfgsb0:armhf. 198s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 198s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 198s Selecting previously unselected package libpython3.12t64:armhf. 198s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_armhf.deb ... 198s Unpacking libpython3.12t64:armhf (3.12.3-1) ... 199s Selecting previously unselected package python-cobra-data. 199s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 199s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 199s Selecting previously unselected package python3-sniffio. 199s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 199s Unpacking python3-sniffio (1.3.0-2) ... 199s Selecting previously unselected package python3-anyio. 199s Preparing to unpack .../15-python3-anyio_4.3.0-1_all.deb ... 199s Unpacking python3-anyio (4.3.0-1) ... 199s Selecting previously unselected package python3-appdirs. 199s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 199s Unpacking python3-appdirs (1.4.4-4) ... 199s Selecting previously unselected package python3-colorama. 199s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 199s Unpacking python3-colorama (0.4.6-4) ... 199s Selecting previously unselected package python3-click. 199s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 199s Unpacking python3-click (8.1.6-2) ... 199s Selecting previously unselected package python3-depinfo. 199s Preparing to unpack .../19-python3-depinfo_2.2.0-2_armhf.deb ... 199s Unpacking python3-depinfo (2.2.0-2) ... 199s Selecting previously unselected package python3-diskcache. 200s Preparing to unpack .../20-python3-diskcache_5.6.3-1_all.deb ... 200s Unpacking python3-diskcache (5.6.3-1) ... 200s Selecting previously unselected package python3-h11. 200s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 200s Unpacking python3-h11 (0.14.0-1) ... 200s Selecting previously unselected package python3-httpcore. 201s Preparing to unpack .../22-python3-httpcore_1.0.4-1_all.deb ... 201s Unpacking python3-httpcore (1.0.4-1) ... 201s Selecting previously unselected package python3-httpx. 201s Preparing to unpack .../23-python3-httpx_0.27.0-1_all.deb ... 201s Unpacking python3-httpx (0.27.0-1) ... 201s Selecting previously unselected package python3-more-itertools. 201s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 201s Unpacking python3-more-itertools (10.2.0-1) ... 201s Selecting previously unselected package python3-zipp. 201s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 201s Unpacking python3-zipp (1.0.0-6) ... 201s Selecting previously unselected package python3-importlib-resources. 201s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 201s Unpacking python3-importlib-resources (6.0.1-1) ... 201s Selecting previously unselected package python3-numpy. 201s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_armhf.deb ... 201s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 201s Selecting previously unselected package python3-swiglpk. 201s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_armhf.deb ... 201s Unpacking python3-swiglpk (5.0.10-1build1) ... 201s Selecting previously unselected package python3-mpmath. 201s Preparing to unpack .../29-python3-mpmath_1.3.0-1_all.deb ... 201s Unpacking python3-mpmath (1.3.0-1) ... 201s Selecting previously unselected package python3-sympy. 202s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 202s Unpacking python3-sympy (1.12-7) ... 202s Selecting previously unselected package python3-optlang. 202s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 202s Unpacking python3-optlang (1.8.1-1) ... 202s Selecting previously unselected package python3-dateutil. 202s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 202s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 202s Selecting previously unselected package python3-pandas-lib:armhf. 202s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_armhf.deb ... 202s Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-7) ... 203s Selecting previously unselected package python3-pandas. 203s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 203s Unpacking python3-pandas (2.1.4+dfsg-7) ... 203s Selecting previously unselected package python3-pydantic. 203s Preparing to unpack .../35-python3-pydantic_1.10.14-1_armhf.deb ... 203s Unpacking python3-pydantic (1.10.14-1) ... 204s Selecting previously unselected package python3-ruamel.yaml.clib:armhf. 204s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8-1build1_armhf.deb ... 204s Unpacking python3-ruamel.yaml.clib:armhf (0.2.8-1build1) ... 204s Selecting previously unselected package python3-ruamel.yaml. 204s Preparing to unpack .../37-python3-ruamel.yaml_0.17.21-1_all.deb ... 204s Unpacking python3-ruamel.yaml (0.17.21-1) ... 204s Selecting previously unselected package python3-simplejson. 204s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_armhf.deb ... 204s Unpacking python3-simplejson (3.19.2-1build2) ... 204s Selecting previously unselected package python3-tabulate. 204s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 204s Unpacking python3-tabulate (0.8.10-1) ... 204s Selecting previously unselected package swig. 204s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_armhf.deb ... 204s Unpacking swig (4.2.0-2ubuntu1) ... 204s Selecting previously unselected package python3-sbml5. 204s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_armhf.deb ... 204s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 204s Selecting previously unselected package python3-cobra. 204s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_armhf.deb ... 204s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 204s Selecting previously unselected package python3-cpuinfo. 204s Preparing to unpack .../43-python3-cpuinfo_9.0.0+git20221119-1_all.deb ... 204s Unpacking python3-cpuinfo (9.0.0+git20221119-1) ... 204s Selecting previously unselected package python3-decorator. 204s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 204s Unpacking python3-decorator (5.1.1-5) ... 204s Selecting previously unselected package python3-iniconfig. 204s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 204s Unpacking python3-iniconfig (1.1.1-2) ... 204s Selecting previously unselected package python3-packaging. 204s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 204s Unpacking python3-packaging (24.0-1) ... 204s Selecting previously unselected package python3-pluggy. 204s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 204s Unpacking python3-pluggy (1.4.0-1) ... 205s Selecting previously unselected package python3-pytest. 205s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 205s Unpacking python3-pytest (7.4.4-1) ... 205s Selecting previously unselected package python3-pytest-benchmark. 205s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 205s Unpacking python3-pytest-benchmark (4.0.0-3) ... 205s Selecting previously unselected package python3-pytest-mock. 205s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 205s Unpacking python3-pytest-mock (3.12.0-1.1) ... 205s Selecting previously unselected package quilt. 205s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 205s Unpacking quilt (0.67+really0.67-4) ... 205s Selecting previously unselected package python3-scipy. 205s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_armhf.deb ... 205s Unpacking python3-scipy (1.11.4-6build1) ... 206s Selecting previously unselected package autopkgtest-satdep. 206s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 206s Unpacking autopkgtest-satdep (0) ... 206s Setting up python3-more-itertools (10.2.0-1) ... 207s Setting up python3-iniconfig (1.1.1-2) ... 207s Setting up python3-sniffio (1.3.0-2) ... 207s Setting up swig (4.2.0-2ubuntu1) ... 207s Setting up python3-anyio (4.3.0-1) ... 207s Setting up python3-colorama (0.4.6-4) ... 207s Setting up python3-ruamel.yaml.clib:armhf (0.2.8-1build1) ... 207s Setting up python3-tabulate (0.8.10-1) ... 208s Setting up python3-zipp (1.0.0-6) ... 208s Setting up libgomp1:armhf (14-20240412-0ubuntu1) ... 208s Setting up python3-click (8.1.6-2) ... 208s Setting up libpython3.12t64:armhf (3.12.3-1) ... 208s Setting up python3-simplejson (3.19.2-1build2) ... 208s Setting up python3-decorator (5.1.1-5) ... 208s Setting up libblas3:armhf (3.12.0-3build1) ... 208s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 208s Setting up python3-packaging (24.0-1) ... 209s Setting up python3-pydantic (1.10.14-1) ... 209s Setting up diffstat (1.66-1build1) ... 209s Setting up python3-h11 (0.14.0-1) ... 209s Setting up python3-depinfo (2.2.0-2) ... 209s Setting up python3-cpuinfo (9.0.0+git20221119-1) ... 209s Setting up libltdl7:armhf (2.4.7-7build1) ... 209s Setting up libgfortran5:armhf (14-20240412-0ubuntu1) ... 209s Setting up python3-pluggy (1.4.0-1) ... 210s Setting up python3-ruamel.yaml (0.17.21-1) ... 210s Setting up libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1build1) ... 210s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 210s Setting up python3-mpmath (1.3.0-1) ... 211s Setting up python3-diskcache (5.6.3-1) ... 211s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 211s Setting up python3-appdirs (1.4.4-4) ... 211s Setting up python3-httpcore (1.0.4-1) ... 211s Setting up python3-sympy (1.12-7) ... 219s Setting up liblapack3:armhf (3.12.0-3build1) ... 219s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 219s Setting up gettext (0.21-14ubuntu2) ... 219s Setting up libamd3:armhf (1:7.6.1+dfsg-1build1) ... 219s Setting up python3-importlib-resources (6.0.1-1) ... 219s Setting up libcolamd3:armhf (1:7.6.1+dfsg-1build1) ... 219s Setting up python3-pytest (7.4.4-1) ... 219s Setting up quilt (0.67+really0.67-4) ... 219s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 220s Setting up python3-httpx (0.27.0-1) ... 220s Setting up libglpk40:armhf (5.0-1build2) ... 220s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 222s Setting up python3-pytest-mock (3.12.0-1.1) ... 223s Setting up python3-swiglpk (5.0.10-1build1) ... 223s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 223s Setting up python3-optlang (1.8.1-1) ... 223s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 223s """A representation of the convex optimizatgion problem in standard form. 223s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 223s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 223s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 223s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 223s Setting up python3-pytest-benchmark (4.0.0-3) ... 223s Setting up python3-scipy (1.11.4-6build1) ... 227s Setting up python3-pandas-lib:armhf (2.1.4+dfsg-7) ... 227s Setting up python3-pandas (2.1.4+dfsg-7) ... 233s Setting up python3-cobra (0.29.0-1ubuntu2) ... 234s Setting up autopkgtest-satdep (0) ... 234s Processing triggers for man-db (2.12.0-4build2) ... 234s Processing triggers for install-info (7.1-3build2) ... 234s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 254s (Reading database ... 65893 files and directories currently installed.) 254s Removing autopkgtest-satdep (0) ... 259s autopkgtest [22:33:30]: test run-unit-test: [----------------------- 261s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 261s Running Tests 261s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 266s ============================= test session starts ============================== 266s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 266s 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) 266s rootdir: /tmp/autopkgtest.htB337/autopkgtest_tmp 266s plugins: anyio-4.3.0, benchmark-4.0.0, mock-3.12.0 266s collected 551 items 266s 266s tests/test_core/test_configuration.py ...... [ 1%] 272s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 273s ...................x....... [ 12%] 273s tests/test_core/test_dictlist.py ...................... [ 16%] 273s tests/test_core/test_formula.py ..... [ 17%] 273s tests/test_core/test_gene.py . [ 17%] 273s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 284s .......................... [ 29%] 284s tests/test_core/test_group.py .. [ 30%] 284s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 294s tests/test_core/test_model.py .......................................... [ 39%] 295s ...........s..s.ss. [ 43%] 295s tests/test_core/test_solution.py .ss [ 43%] 302s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 304s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 308s tests/test_flux_analysis/test_geometric.py .. [ 46%] 308s tests/test_flux_analysis/test_moma.py . [ 46%] 313s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 313s tests/test_flux_analysis/test_reaction.py . [ 47%] 316s tests/test_flux_analysis/test_room.py .... [ 47%] 326s tests/test_flux_analysis/test_variability.py ....... [ 49%] 326s tests/test_flux_analysis/test_deletion.py sss [ 49%] 326s tests/test_flux_analysis/test_moma.py s [ 49%] 337s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 341s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 341s tests/test_flux_analysis/test_helpers.py ... [ 51%] 342s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 345s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 347s tests/test_flux_analysis/test_variability.py ....... [ 54%] 347s tests/test_io/test_annotation.py .. [ 55%] 347s tests/test_io/test_annotation_format.py .. [ 55%] 353s tests/test_io/test_io_order.py ........................... [ 60%] 353s tests/test_io/test_json.py .... [ 61%] 358s tests/test_io/test_mat.py .......ssss.... [ 64%] 358s tests/test_io/test_notes.py . [ 64%] 358s tests/test_io/test_pickle.py .. [ 64%] 366s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 367s tests/test_io/test_yaml.py .x [ 72%] 368s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 368s tests/test_manipulation/test_annotate.py . [ 73%] 368s tests/test_manipulation/test_delete.py ....... [ 75%] 369s tests/test_manipulation/test_modify.py ... [ 75%] 369s tests/test_manipulation/test_validate.py .. [ 76%] 369s tests/test_medium/test_boundary_types.py ......... [ 77%] 372s tests/test_medium/test_minimal_medium.py .......... [ 79%] 374s tests/test_sampling/test_achr.py ...... [ 80%] 376s tests/test_sampling/test_optgp.py ...... [ 81%] 383s tests/test_sampling/test_sampling.py .......... [ 83%] 387s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 390s tests/test_summary/test_model_summary.py ............... [ 89%] 392s tests/test_summary/test_reaction_summary.py .................... [ 92%] 392s tests/test_util/test_array.py .. [ 93%] 392s tests/test_util/test_context.py ... [ 93%] 395s tests/test_util/test_process_pool.py ............... [ 96%] 396s tests/test_util/test_solver.py ..............s [ 99%] 396s tests/test_util/test_util.py ...X [100%] 396s 396s =============================== warnings summary =============================== 396s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 396s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 396s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 396s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 396s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 396s /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)'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 396s warn( 396s 396s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 396s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 396s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 396s warn( 396s 396s tests/test_core/test_model.py::test_reaction_delete 396s tests/test_core/test_model.py::test_reaction_delete 396s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 396s warn( 396s 396s tests/test_core/test_model.py::test_group_loss_of_elements 396s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 396s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 396s warn("need to pass in a list") 396s 396s tests/test_core/test_model.py::test_change_objective 396s tests/test_core/test_model.py::test_change_objective 396s tests/test_core/test_model.py::test_change_objective 396s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 396s warn("Please use reaction.flux instead.", DeprecationWarning) 396s 396s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 396s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 396s /tmp/autopkgtest.htB337/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 396s assert math.isnan(sol.growth) 396s 396s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 396s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 396s /tmp/autopkgtest.htB337/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 396s assert math.isnan(sol_one.growth) 396s 396s tests/test_io/test_json.py: 1 warning 396s tests/test_io/test_mat.py: 3 warnings 396s tests/test_io/test_pickle.py: 1 warning 396s tests/test_io/test_sbml.py: 9 warnings 396s tests/test_io/test_yaml.py: 1 warning 396s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 396s warn(f"Solver status is '{status}'.", UserWarning) 396s 396s tests/test_medium/test_boundary_types.py: 96 warnings 396s /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]` 396s return most[0] 396s 396s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 396s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 396s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 396s /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]` 396s compartment = most[matches[most]][0] 396s 396s tests/test_util/test_process_pool.py::test_with_context 396s /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 396s self._pool.__enter__() 396s 396s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 396s 396s --------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests ---------------------------------------------------------------------------------------------------------------------- 396s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 396s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 396s test_subtract_metabolite_benchmark[glpk] 3.7600 (1.0) 36.8410 (1.0) 4.0400 (1.01) 1.0605 (1.06) 3.9200 (1.0) 0.1200 (1.50) 28;442 247,524.9924 (0.99) 2931 1 396s test_subtract_metabolite_benchmark[cplex] 3.8000 (1.01) 52.2800 (1.42) 3.9861 (1.0) 1.0032 (1.0) 3.9200 (1.0) 0.0800 (1.0) 17;182 250,871.9621 (1.0) 3090 1 396s test_subtract_metabolite_benchmark[gurobi] 3.8000 (1.01) 53.3610 (1.45) 4.0999 (1.03) 1.3030 (1.30) 3.9600 (1.01) 0.1600 (2.00) 18;204 243,907.7431 (0.97) 2379 1 396s test_change_objective_benchmark[optlang-glpk] 196.4420 (52.25) 1,850.7780 (50.24) 216.3915 (54.29) 44.8202 (44.68) 205.4820 (52.42) 10.0400 (125.49) 178;400 4,621.2529 (0.02) 2374 1 396s test_achr_sample_benchmark 212.1620 (56.43) 546.5250 (14.83) 242.5361 (60.85) 31.4170 (31.32) 229.5020 (58.55) 16.8000 (209.98) 123;141 4,123.0967 (0.02) 768 1 396s test_optgp_sample_benchmark 318.3630 (84.67) 589.6450 (16.01) 360.4259 (90.42) 46.7085 (46.56) 339.2230 (86.54) 41.6410 (520.47) 30;16 2,774.4954 (0.01) 186 1 396s test_loopless_benchmark_after 1,384.1730 (368.13) 2,124.3790 (57.66) 1,529.9445 (383.82) 99.2170 (98.90) 1,519.1340 (387.53) 137.8910 (>1000.0) 86;2 653.6185 (0.00) 279 1 396s test_loopless_benchmark_before 6,191.9370 (>1000.0) 7,329.3080 (198.94) 6,546.5366 (>1000.0) 269.7295 (268.87) 6,465.2590 (>1000.0) 363.8930 (>1000.0) 13;1 152.7525 (0.00) 51 1 396s test_minimal_medium_mip_benchmark 11,562.7870 (>1000.0) 69,061.0380 (>1000.0) 12,750.1452 (>1000.0) 7,331.0604 (>1000.0) 11,789.5090 (>1000.0) 201.3220 (>1000.0) 1;1 78.4305 (0.00) 61 1 396s test_minimal_medium_linear_benchmark 11,806.6290 (>1000.0) 61,377.8870 (>1000.0) 12,967.0679 (>1000.0) 6,536.8466 (>1000.0) 12,001.3510 (>1000.0) 250.9930 (>1000.0) 1;3 77.1184 (0.00) 57 1 396s test_copy_benchmark[optlang-glpk] 17,152.6390 (>1000.0) 418,123.6320 (>1000.0) 26,931.6029 (>1000.0) 56,468.4095 (>1000.0) 18,451.3110 (>1000.0) 2,054.5390 (>1000.0) 1;2 37.1311 (0.00) 50 1 396s test_deepcopy_benchmark 27,379.1730 (>1000.0) 661,125.1600 (>1000.0) 48,335.0040 (>1000.0) 106,640.8829 (>1000.0) 30,355.5610 (>1000.0) 3,271.8095 (>1000.0) 1;1 20.6889 (0.00) 35 1 396s test_gpr_equality_benchmark 27,643.6960 (>1000.0) 30,136.3990 (818.01) 28,379.7348 (>1000.0) 634.4796 (632.45) 28,296.9420 (>1000.0) 690.6460 (>1000.0) 10;2 35.2364 (0.00) 30 1 396s test_single_reaction_deletion_benchmark[glpk] 28,122.2600 (>1000.0) 29,849.6360 (810.23) 28,853.3920 (>1000.0) 548.1977 (546.44) 28,921.3475 (>1000.0) 975.2890 (>1000.0) 14;0 34.6580 (0.00) 32 1 396s test_add_metabolite_benchmark[gurobi] 64,109.5940 (>1000.0) 69,215.6010 (>1000.0) 65,471.3088 (>1000.0) 1,236.5739 (>1000.0) 65,162.6030 (>1000.0) 1,008.2295 (>1000.0) 3;1 15.2739 (0.00) 16 1 396s test_add_metabolite_benchmark[glpk] 64,750.8400 (>1000.0) 71,738.3050 (>1000.0) 66,642.4025 (>1000.0) 1,808.7952 (>1000.0) 65,928.6110 (>1000.0) 1,908.6975 (>1000.0) 3;1 15.0055 (0.00) 16 1 396s test_add_metabolite_benchmark[cplex] 64,843.3610 (>1000.0) 66,100.8120 (>1000.0) 65,501.6618 (>1000.0) 365.6774 (364.51) 65,533.7875 (>1000.0) 613.5255 (>1000.0) 5;0 15.2668 (0.00) 16 1 396s test_fastcc_benchmark[glpk] 66,329.6130 (>1000.0) 76,454.6670 (>1000.0) 70,093.7069 (>1000.0) 3,921.6845 (>1000.0) 67,905.1890 (>1000.0) 6,563.5500 (>1000.0) 2;0 14.2666 (0.00) 13 1 396s test_optgp_init_benchmark 99,758.4410 (>1000.0) 132,821.7860 (>1000.0) 104,594.1378 (>1000.0) 9,983.1422 (>1000.0) 101,653.8185 (>1000.0) 1,849.2170 (>1000.0) 1;1 9.5608 (0.00) 10 1 396s test_achr_init_benchmark 100,173.7650 (>1000.0) 155,256.8740 (>1000.0) 114,356.1227 (>1000.0) 22,161.2889 (>1000.0) 102,739.8490 (>1000.0) 24,592.3870 (>1000.0) 1;0 8.7446 (0.00) 6 1 396s test_single_gene_deletion_fba_benchmark[glpk] 157,900.4610 (>1000.0) 305,894.5110 (>1000.0) 192,852.2783 (>1000.0) 55,908.7721 (>1000.0) 174,320.9735 (>1000.0) 13,537.7650 (>1000.0) 1;1 5.1853 (0.00) 6 1 396s test_single_gene_deletion_linear_moma_benchmark[glpk] 185,029.7130 (>1000.0) 193,554.5110 (>1000.0) 189,158.2468 (>1000.0) 4,227.9519 (>1000.0) 188,553.4250 (>1000.0) 8,379.8973 (>1000.0) 2;0 5.2866 (0.00) 5 1 396s test_gpr_symbolism_benchmark 186,204.2450 (>1000.0) 193,701.7540 (>1000.0) 190,689.0462 (>1000.0) 3,350.5277 (>1000.0) 192,504.8630 (>1000.0) 5,603.0210 (>1000.0) 1;0 5.2441 (0.00) 5 1 396s test_flux_variability_loopless_benchmark[glpk] 201,110.7390 (>1000.0) 392,374.2690 (>1000.0) 266,090.1140 (>1000.0) 74,140.7237 (>1000.0) 230,450.0910 (>1000.0) 96,868.0160 (>1000.0) 1;0 3.7581 (0.00) 6 1 396s test_single_gene_deletion_linear_room_benchmark[glpk] 298,106.3590 (>1000.0) 684,387.7340 (>1000.0) 377,519.9820 (>1000.0) 171,564.7604 (>1000.0) 301,052.7860 (>1000.0) 101,041.2850 (>1000.0) 1;1 2.6489 (0.00) 5 1 396s test_pfba_benchmark[glpk] 320,045.9200 (>1000.0) 688,321.6880 (>1000.0) 395,523.2988 (>1000.0) 163,694.5290 (>1000.0) 323,593.0740 (>1000.0) 95,843.8165 (>1000.0) 1;1 2.5283 (0.00) 5 1 396s test_copy_benchmark_large_model[optlang-glpk] 353,171.7900 (>1000.0) 894,641.4030 (>1000.0) 559,766.2784 (>1000.0) 279,592.8048 (>1000.0) 358,940.9630 (>1000.0) 494,904.2017 (>1000.0) 1;0 1.7865 (0.00) 5 1 396s test_double_gene_deletion_benchmark 373,085.4100 (>1000.0) 391,720.2220 (>1000.0) 381,512.6878 (>1000.0) 8,078.2523 (>1000.0) 377,182.1680 (>1000.0) 13,131.6817 (>1000.0) 2;0 2.6211 (0.00) 5 1 396s test_geometric_fba_benchmark[glpk] 438,761.5400 (>1000.0) 471,648.2840 (>1000.0) 453,927.5764 (>1000.0) 14,366.9884 (>1000.0) 459,876.5360 (>1000.0) 23,594.4285 (>1000.0) 3;0 2.2030 (0.00) 5 1 396s test_double_reaction_deletion_benchmark 512,027.3730 (>1000.0) 1,012,068.6360 (>1000.0) 705,299.6478 (>1000.0) 215,655.0610 (>1000.0) 587,834.9140 (>1000.0) 339,151.2757 (>1000.0) 1;0 1.4178 (0.00) 5 1 396s test_flux_variability_benchmark[glpk] 682,726.7950 (>1000.0) 688,873.5310 (>1000.0) 686,181.2586 (>1000.0) 2,510.5444 (>1000.0) 687,176.7960 (>1000.0) 3,911.0858 (>1000.0) 2;0 1.4573 (0.00) 5 1 396s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 396s 396s Legend: 396s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 396s OPS: Operations Per Second, computed as 1 / Mean 396s = 509 passed, 31 skipped, 10 xfailed, 1 xpassed, 169 warnings in 131.74s (0:02:11) = 399s Removing patch debian/patches/no_future_dependency.patch 399s Restoring setup.cfg 399s 399s Removing patch debian/patches/32-bit-test.patch 399s Restoring tests/test_io/test_mat.py 399s 399s Removing patch debian/patches/do-not-seek-for-name.patch 399s Restoring src/cobra/io/sbml.py 399s 399s Removing patch debian/patches/ignore_tests.patch 399s Restoring tests/test_io/test_web/test_load.py 400s 400s Removing patch debian/patches/xfail_test_show_versions.patch 400s Restoring tests/test_util/test_util.py 400s 400s Removing patch debian/patches/mathjax.patch 400s Restoring documentation_builder/conf.py 400s 400s No patches applied 400s PASS 400s autopkgtest [22:35:51]: test run-unit-test: -----------------------] 404s autopkgtest [22:35:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 404s run-unit-test PASS 408s autopkgtest [22:35:59]: @@@@@@@@@@@@@@@@@@@@ summary 408s run-unit-test PASS