0s autopkgtest [19:58:40]: starting date and time: 2024-05-15 19:58:40+0000 0s autopkgtest [19:58:40]: git checkout: d60bd36 autopkgtest-build-lxd: Add missing remote prefix in get_boot_id(). 0s autopkgtest [19:58:40]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3re8puqx/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:ruamel.yaml,src:ruamel.yaml.clib --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 ruamel.yaml.clib/0.2.8+ds-1' -- lxd -r lxd-armhf-10.145.243.92 lxd-armhf-10.145.243.92:autopkgtest/ubuntu/oracular/armhf 31s autopkgtest [19:59:10]: testbed dpkg architecture: armhf 32s autopkgtest [19:59:12]: testbed apt version: 2.7.14build2 32s autopkgtest [19:59:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 40s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 40s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1842 kB] 40s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [9628 B] 40s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [137 kB] 40s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [199 kB] 40s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [1301 kB] 40s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [6188 B] 40s Fetched 3570 kB in 1s (2985 kB/s) 40s Reading package lists... 56s tee: /proc/self/fd/2: Permission denied 78s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Calculating upgrade... 80s The following packages will be upgraded: 80s libgnutls30t64 pastebinit 80s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 973 kB of archives. 80s After this operation, 24.6 kB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf libgnutls30t64 armhf 3.8.5-2ubuntu1 [958 kB] 81s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf pastebinit all 1.7.0-1 [14.9 kB] 81s Fetched 973 kB in 1s (1593 kB/s) 81s (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.) 81s Preparing to unpack .../libgnutls30t64_3.8.5-2ubuntu1_armhf.deb ... 81s Unpacking libgnutls30t64:armhf (3.8.5-2ubuntu1) over (3.8.3-1.1ubuntu3.1) ... 81s Setting up libgnutls30t64:armhf (3.8.5-2ubuntu1) ... 82s (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.) 82s Preparing to unpack .../pastebinit_1.7.0-1_all.deb ... 82s Unpacking pastebinit (1.7.0-1) over (1.6.2-1) ... 82s Setting up pastebinit (1.7.0-1) ... 82s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 82s Processing triggers for man-db (2.12.0-4build2) ... 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s autopkgtest [20:00:05]: rebooting testbed after setup commands that affected boot 124s autopkgtest [20:00:44]: testbed running kernel: Linux 5.15.0-106-generic #116-Ubuntu SMP Wed Apr 17 09:19:22 UTC 2024 149s autopkgtest [20:01:09]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 163s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 163s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 163s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 164s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 164s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 164s gpgv: Can't check signature: No public key 164s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 164s autopkgtest [20:01:24]: testing package python-cobra version 0.29.0-1ubuntu2 166s autopkgtest [20:01:26]: build not needed 168s autopkgtest [20:01:28]: test run-unit-test: preparing testbed 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 181s Starting pkgProblemResolver with broken count: 0 181s Starting 2 pkgProblemResolver with broken count: 0 181s Done 183s The following additional packages will be installed: 183s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 183s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 183s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 183s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 183s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 183s python3-importlib-resources python3-iniconfig python3-more-itertools 183s python3-mpmath python3-numpy python3-optlang python3-packaging 183s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 183s python3-pytest python3-pytest-benchmark python3-pytest-mock 183s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 183s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 183s python3-tabulate python3-zipp quilt swig 183s Suggested packages: 183s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 183s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 183s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 183s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 183s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 183s swig-doc swig-examples 183s Recommended packages: 183s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 183s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 183s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 183s python3-pil isympy-common 183s The following NEW packages will be installed: 183s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 183s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 183s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 183s python3-click python3-cobra python3-colorama python3-cpuinfo 183s python3-dateutil python3-decorator python3-depinfo python3-diskcache 183s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 183s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 183s python3-optlang python3-packaging python3-pandas python3-pandas-lib 183s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 183s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 183s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 183s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 183s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 47.5 MB/47.5 MB of archives. 183s After this operation, 195 MB of additional disk space will be used. 183s Get:1 /tmp/autopkgtest.QzeQlX/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [764 B] 183s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf diffstat armhf 1.66-1build1 [27.7 kB] 183s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libgomp1 armhf 14-20240412-0ubuntu1 [125 kB] 184s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf gettext armhf 0.21-14ubuntu2 [800 kB] 184s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libsuitesparseconfig7 armhf 1:7.6.1+dfsg-1build1 [12.1 kB] 184s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libamd3 armhf 1:7.6.1+dfsg-1build1 [28.2 kB] 184s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 184s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf libcolamd3 armhf 1:7.6.1+dfsg-1build1 [20.1 kB] 184s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14-20240412-0ubuntu1 [316 kB] 184s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf libltdl7 armhf 2.4.7-7build1 [37.6 kB] 184s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 184s Get:12 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 184s Get:13 http://ftpmaster.internal/ubuntu oracular/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 184s Get:14 http://ftpmaster.internal/ubuntu oracular/main armhf libpython3.12t64 armhf 3.12.3-1 [2058 kB] 184s Get:15 http://ftpmaster.internal/ubuntu oracular/universe armhf python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 184s Get:16 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sniffio all 1.3.0-2 [7216 B] 184s Get:17 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-anyio all 4.3.0-1 [56.6 kB] 184s Get:18 http://ftpmaster.internal/ubuntu oracular/main armhf python3-appdirs all 1.4.4-4 [10.9 kB] 184s Get:19 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 184s Get:20 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.6-2 [79.0 kB] 184s Get:21 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-depinfo armhf 2.2.0-2 [10.9 kB] 184s Get:22 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-diskcache all 5.6.3-1 [35.1 kB] 184s Get:23 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-h11 all 0.14.0-1 [51.1 kB] 184s Get:24 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-httpcore all 1.0.4-1 [38.8 kB] 184s Get:25 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-httpx all 0.26.0-2 [61.3 kB] 184s Get:26 http://ftpmaster.internal/ubuntu oracular/main armhf python3-more-itertools all 10.2.0-1 [52.9 kB] 184s Get:27 http://ftpmaster.internal/ubuntu oracular/main armhf python3-zipp all 1.0.0-6 [6090 B] 184s Get:28 http://ftpmaster.internal/ubuntu oracular/main armhf python3-importlib-resources all 6.0.1-1 [22.1 kB] 184s Get:29 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-6ubuntu1 [3541 kB] 184s Get:30 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-swiglpk armhf 5.0.10-1build1 [66.3 kB] 184s Get:31 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 184s Get:32 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sympy all 1.12-7 [3966 kB] 184s Get:33 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-optlang all 1.8.1-1 [82.7 kB] 184s Get:34 http://ftpmaster.internal/ubuntu oracular/main armhf python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 184s Get:35 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pandas-lib armhf 2.1.4+dfsg-7 [4462 kB] 184s Get:36 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pandas all 2.1.4+dfsg-7 [3042 kB] 184s Get:37 http://ftpmaster.internal/ubuntu oracular/main armhf python3-pydantic armhf 1.10.14-1 [1738 kB] 184s Get:38 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-ruamel.yaml.clib armhf 0.2.8+ds-1 [120 kB] 184s Get:39 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 184s Get:40 http://ftpmaster.internal/ubuntu oracular/main armhf python3-simplejson armhf 3.19.2-1build2 [52.0 kB] 184s Get:41 http://ftpmaster.internal/ubuntu oracular/main armhf python3-tabulate all 0.8.10-1 [38.2 kB] 184s Get:42 http://ftpmaster.internal/ubuntu oracular/universe armhf swig armhf 4.2.0-2ubuntu1 [1115 kB] 185s Get:43 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-sbml5 armhf 5.20.2+dfsg-3 [3497 kB] 185s Get:44 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cobra armhf 0.29.0-1ubuntu2 [1119 kB] 185s Get:45 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cpuinfo all 9.0.0+git20221119-1 [21.4 kB] 185s Get:46 http://ftpmaster.internal/ubuntu oracular/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 185s Get:47 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 185s Get:48 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.0-1 [41.1 kB] 185s Get:49 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.4.0-1 [20.4 kB] 185s Get:50 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest all 7.4.4-1 [305 kB] 185s Get:51 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 185s Get:52 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 185s Get:53 http://ftpmaster.internal/ubuntu oracular/universe armhf quilt all 0.67+really0.67-4 [436 kB] 185s Get:54 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-scipy armhf 1.11.4-6build1 [15.1 MB] 186s Fetched 47.5 MB in 2s (22.8 MB/s) 186s Selecting previously unselected package diffstat. 186s (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 ... 57883 files and directories currently installed.) 186s Preparing to unpack .../00-diffstat_1.66-1build1_armhf.deb ... 186s Unpacking diffstat (1.66-1build1) ... 186s Selecting previously unselected package libgomp1:armhf. 186s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_armhf.deb ... 186s Unpacking libgomp1:armhf (14-20240412-0ubuntu1) ... 186s Selecting previously unselected package gettext. 186s Preparing to unpack .../02-gettext_0.21-14ubuntu2_armhf.deb ... 186s Unpacking gettext (0.21-14ubuntu2) ... 186s Selecting previously unselected package libsuitesparseconfig7:armhf. 186s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_armhf.deb ... 186s Unpacking libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1build1) ... 186s Selecting previously unselected package libamd3:armhf. 187s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_armhf.deb ... 187s Unpacking libamd3:armhf (1:7.6.1+dfsg-1build1) ... 187s Selecting previously unselected package libblas3:armhf. 187s Preparing to unpack .../05-libblas3_3.12.0-3build1_armhf.deb ... 187s Unpacking libblas3:armhf (3.12.0-3build1) ... 187s Selecting previously unselected package libcolamd3:armhf. 187s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_armhf.deb ... 187s Unpacking libcolamd3:armhf (1:7.6.1+dfsg-1build1) ... 187s Selecting previously unselected package libgfortran5:armhf. 187s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_armhf.deb ... 187s Unpacking libgfortran5:armhf (14-20240412-0ubuntu1) ... 187s Selecting previously unselected package libltdl7:armhf. 187s Preparing to unpack .../08-libltdl7_2.4.7-7build1_armhf.deb ... 187s Unpacking libltdl7:armhf (2.4.7-7build1) ... 187s Selecting previously unselected package libglpk40:armhf. 187s Preparing to unpack .../09-libglpk40_5.0-1build2_armhf.deb ... 187s Unpacking libglpk40:armhf (5.0-1build2) ... 187s Selecting previously unselected package liblapack3:armhf. 187s Preparing to unpack .../10-liblapack3_3.12.0-3build1_armhf.deb ... 187s Unpacking liblapack3:armhf (3.12.0-3build1) ... 187s Selecting previously unselected package liblbfgsb0:armhf. 187s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 187s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 187s Selecting previously unselected package libpython3.12t64:armhf. 187s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_armhf.deb ... 187s Unpacking libpython3.12t64:armhf (3.12.3-1) ... 187s Selecting previously unselected package python-cobra-data. 187s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 187s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 187s Selecting previously unselected package python3-sniffio. 187s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 187s Unpacking python3-sniffio (1.3.0-2) ... 187s Selecting previously unselected package python3-anyio. 187s Preparing to unpack .../15-python3-anyio_4.3.0-1_all.deb ... 187s Unpacking python3-anyio (4.3.0-1) ... 187s Selecting previously unselected package python3-appdirs. 187s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 187s Unpacking python3-appdirs (1.4.4-4) ... 187s Selecting previously unselected package python3-colorama. 187s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 187s Unpacking python3-colorama (0.4.6-4) ... 187s Selecting previously unselected package python3-click. 187s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 187s Unpacking python3-click (8.1.6-2) ... 187s Selecting previously unselected package python3-depinfo. 187s Preparing to unpack .../19-python3-depinfo_2.2.0-2_armhf.deb ... 187s Unpacking python3-depinfo (2.2.0-2) ... 187s Selecting previously unselected package python3-diskcache. 187s Preparing to unpack .../20-python3-diskcache_5.6.3-1_all.deb ... 187s Unpacking python3-diskcache (5.6.3-1) ... 187s Selecting previously unselected package python3-h11. 188s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 188s Unpacking python3-h11 (0.14.0-1) ... 188s Selecting previously unselected package python3-httpcore. 188s Preparing to unpack .../22-python3-httpcore_1.0.4-1_all.deb ... 188s Unpacking python3-httpcore (1.0.4-1) ... 188s Selecting previously unselected package python3-httpx. 188s Preparing to unpack .../23-python3-httpx_0.26.0-2_all.deb ... 188s Unpacking python3-httpx (0.26.0-2) ... 188s Selecting previously unselected package python3-more-itertools. 188s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 188s Unpacking python3-more-itertools (10.2.0-1) ... 188s Selecting previously unselected package python3-zipp. 188s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 188s Unpacking python3-zipp (1.0.0-6) ... 188s Selecting previously unselected package python3-importlib-resources. 188s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 188s Unpacking python3-importlib-resources (6.0.1-1) ... 188s Selecting previously unselected package python3-numpy. 188s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_armhf.deb ... 188s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 188s Selecting previously unselected package python3-swiglpk. 188s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_armhf.deb ... 188s Unpacking python3-swiglpk (5.0.10-1build1) ... 188s Selecting previously unselected package python3-mpmath. 188s Preparing to unpack .../29-python3-mpmath_1.3.0-1_all.deb ... 188s Unpacking python3-mpmath (1.3.0-1) ... 188s Selecting previously unselected package python3-sympy. 188s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 188s Unpacking python3-sympy (1.12-7) ... 189s Selecting previously unselected package python3-optlang. 189s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 189s Unpacking python3-optlang (1.8.1-1) ... 189s Selecting previously unselected package python3-dateutil. 189s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 189s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 189s Selecting previously unselected package python3-pandas-lib:armhf. 189s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_armhf.deb ... 189s Unpacking python3-pandas-lib:armhf (2.1.4+dfsg-7) ... 189s Selecting previously unselected package python3-pandas. 189s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 189s Unpacking python3-pandas (2.1.4+dfsg-7) ... 190s Selecting previously unselected package python3-pydantic. 191s Preparing to unpack .../35-python3-pydantic_1.10.14-1_armhf.deb ... 191s Unpacking python3-pydantic (1.10.14-1) ... 191s Selecting previously unselected package python3-ruamel.yaml.clib:armhf. 191s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8+ds-1_armhf.deb ... 191s Unpacking python3-ruamel.yaml.clib:armhf (0.2.8+ds-1) ... 191s Selecting previously unselected package python3-ruamel.yaml. 191s Preparing to unpack .../37-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 191s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 191s Selecting previously unselected package python3-simplejson. 191s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_armhf.deb ... 191s Unpacking python3-simplejson (3.19.2-1build2) ... 191s Selecting previously unselected package python3-tabulate. 191s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 191s Unpacking python3-tabulate (0.8.10-1) ... 191s Selecting previously unselected package swig. 191s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_armhf.deb ... 191s Unpacking swig (4.2.0-2ubuntu1) ... 191s Selecting previously unselected package python3-sbml5. 191s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_armhf.deb ... 191s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 191s Selecting previously unselected package python3-cobra. 191s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_armhf.deb ... 191s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 191s Selecting previously unselected package python3-cpuinfo. 191s Preparing to unpack .../43-python3-cpuinfo_9.0.0+git20221119-1_all.deb ... 191s Unpacking python3-cpuinfo (9.0.0+git20221119-1) ... 191s Selecting previously unselected package python3-decorator. 191s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 191s Unpacking python3-decorator (5.1.1-5) ... 191s Selecting previously unselected package python3-iniconfig. 191s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 191s Unpacking python3-iniconfig (1.1.1-2) ... 191s Selecting previously unselected package python3-packaging. 191s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 191s Unpacking python3-packaging (24.0-1) ... 191s Selecting previously unselected package python3-pluggy. 191s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 191s Unpacking python3-pluggy (1.4.0-1) ... 191s Selecting previously unselected package python3-pytest. 191s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 191s Unpacking python3-pytest (7.4.4-1) ... 191s Selecting previously unselected package python3-pytest-benchmark. 191s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 191s Unpacking python3-pytest-benchmark (4.0.0-3) ... 191s Selecting previously unselected package python3-pytest-mock. 191s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 191s Unpacking python3-pytest-mock (3.12.0-1.1) ... 191s Selecting previously unselected package quilt. 191s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 191s Unpacking quilt (0.67+really0.67-4) ... 191s Selecting previously unselected package python3-scipy. 191s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_armhf.deb ... 191s Unpacking python3-scipy (1.11.4-6build1) ... 191s Selecting previously unselected package autopkgtest-satdep. 191s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 191s Unpacking autopkgtest-satdep (0) ... 191s Setting up python3-more-itertools (10.2.0-1) ... 192s Setting up python3-iniconfig (1.1.1-2) ... 192s Setting up python3-sniffio (1.3.0-2) ... 192s Setting up swig (4.2.0-2ubuntu1) ... 192s Setting up python3-anyio (4.3.0-1) ... 192s Setting up python3-colorama (0.4.6-4) ... 192s Setting up python3-ruamel.yaml.clib:armhf (0.2.8+ds-1) ... 192s Setting up python3-tabulate (0.8.10-1) ... 193s Setting up python3-zipp (1.0.0-6) ... 193s Setting up libgomp1:armhf (14-20240412-0ubuntu1) ... 193s Setting up python3-click (8.1.6-2) ... 193s Setting up libpython3.12t64:armhf (3.12.3-1) ... 193s Setting up python3-simplejson (3.19.2-1build2) ... 193s Setting up python3-decorator (5.1.1-5) ... 193s Setting up libblas3:armhf (3.12.0-3build1) ... 193s 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 193s Setting up python3-packaging (24.0-1) ... 194s Setting up python3-pydantic (1.10.14-1) ... 194s Setting up diffstat (1.66-1build1) ... 194s Setting up python3-h11 (0.14.0-1) ... 194s Setting up python3-depinfo (2.2.0-2) ... 194s Setting up python3-cpuinfo (9.0.0+git20221119-1) ... 195s Setting up libltdl7:armhf (2.4.7-7build1) ... 195s Setting up libgfortran5:armhf (14-20240412-0ubuntu1) ... 195s Setting up python3-pluggy (1.4.0-1) ... 195s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 195s Setting up libsuitesparseconfig7:armhf (1:7.6.1+dfsg-1build1) ... 195s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 195s Setting up python3-mpmath (1.3.0-1) ... 196s Setting up python3-diskcache (5.6.3-1) ... 196s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 196s Setting up python3-appdirs (1.4.4-4) ... 196s Setting up python3-httpcore (1.0.4-1) ... 197s Setting up python3-sympy (1.12-7) ... 203s Setting up liblapack3:armhf (3.12.0-3build1) ... 203s 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 203s Setting up gettext (0.21-14ubuntu2) ... 203s Setting up libamd3:armhf (1:7.6.1+dfsg-1build1) ... 203s Setting up python3-importlib-resources (6.0.1-1) ... 204s Setting up libcolamd3:armhf (1:7.6.1+dfsg-1build1) ... 204s Setting up python3-pytest (7.4.4-1) ... 204s Setting up quilt (0.67+really0.67-4) ... 204s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 204s Setting up python3-httpx (0.26.0-2) ... 205s Setting up libglpk40:armhf (5.0-1build2) ... 205s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 207s Setting up python3-pytest-mock (3.12.0-1.1) ... 207s Setting up python3-swiglpk (5.0.10-1build1) ... 207s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 207s Setting up python3-optlang (1.8.1-1) ... 207s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 207s """A representation of the convex optimizatgion problem in standard form. 207s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 207s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 207s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 207s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 208s Setting up python3-pytest-benchmark (4.0.0-3) ... 208s Setting up python3-scipy (1.11.4-6build1) ... 212s Setting up python3-pandas-lib:armhf (2.1.4+dfsg-7) ... 212s Setting up python3-pandas (2.1.4+dfsg-7) ... 218s Setting up python3-cobra (0.29.0-1ubuntu2) ... 218s Setting up autopkgtest-satdep (0) ... 218s Processing triggers for man-db (2.12.0-4build2) ... 219s Processing triggers for install-info (7.1-3build2) ... 219s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 239s (Reading database ... 65914 files and directories currently installed.) 239s Removing autopkgtest-satdep (0) ... 244s autopkgtest [20:02:44]: test run-unit-test: [----------------------- 247s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 247s Running Tests 247s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 252s ============================= test session starts ============================== 252s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 252s 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) 252s rootdir: /tmp/autopkgtest.QzeQlX/autopkgtest_tmp 252s plugins: anyio-4.3.0, benchmark-4.0.0, mock-3.12.0 252s collected 551 items 252s 253s tests/test_core/test_configuration.py ...... [ 1%] 258s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 259s ...................x....... [ 12%] 259s tests/test_core/test_dictlist.py ...................... [ 16%] 259s tests/test_core/test_formula.py ..... [ 17%] 259s tests/test_core/test_gene.py . [ 17%] 259s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 269s .......................... [ 29%] 269s tests/test_core/test_group.py .. [ 30%] 269s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 278s tests/test_core/test_model.py .......................................... [ 39%] 279s ...........s..s.ss. [ 43%] 279s tests/test_core/test_solution.py .ss [ 43%] 285s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 286s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 289s tests/test_flux_analysis/test_geometric.py .. [ 46%] 290s tests/test_flux_analysis/test_moma.py . [ 46%] 294s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 294s tests/test_flux_analysis/test_reaction.py . [ 47%] 297s tests/test_flux_analysis/test_room.py .... [ 47%] 303s tests/test_flux_analysis/test_variability.py ....... [ 49%] 303s tests/test_flux_analysis/test_deletion.py sss [ 49%] 304s tests/test_flux_analysis/test_moma.py s [ 49%] 311s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 314s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 314s tests/test_flux_analysis/test_helpers.py ... [ 51%] 315s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 318s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 320s tests/test_flux_analysis/test_variability.py ....... [ 54%] 320s tests/test_io/test_annotation.py .. [ 55%] 320s tests/test_io/test_annotation_format.py .. [ 55%] 323s tests/test_io/test_io_order.py ........................... [ 60%] 323s tests/test_io/test_json.py .... [ 61%] 325s tests/test_io/test_mat.py .......ssss.... [ 64%] 325s tests/test_io/test_notes.py . [ 64%] 325s tests/test_io/test_pickle.py .. [ 64%] 332s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 332s tests/test_io/test_yaml.py .x [ 72%] 333s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 333s tests/test_manipulation/test_annotate.py . [ 73%] 333s tests/test_manipulation/test_delete.py ....... [ 75%] 333s tests/test_manipulation/test_modify.py ... [ 75%] 333s tests/test_manipulation/test_validate.py .. [ 76%] 334s tests/test_medium/test_boundary_types.py ......... [ 77%] 336s tests/test_medium/test_minimal_medium.py .......... [ 79%] 338s tests/test_sampling/test_achr.py ...... [ 80%] 340s tests/test_sampling/test_optgp.py ...... [ 81%] 346s tests/test_sampling/test_sampling.py .......... [ 83%] 348s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 351s tests/test_summary/test_model_summary.py ............... [ 89%] 352s tests/test_summary/test_reaction_summary.py .................... [ 92%] 352s tests/test_util/test_array.py .. [ 93%] 352s tests/test_util/test_context.py ... [ 93%] 353s tests/test_util/test_process_pool.py ............... [ 96%] 354s tests/test_util/test_solver.py ..............s [ 99%] 354s tests/test_util/test_util.py ...X [100%] 354s 354s =============================== warnings summary =============================== 354s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 354s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 354s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 354s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 354s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 354s /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)'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 354s warn( 354s 354s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 354s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 354s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 354s warn( 354s 354s tests/test_core/test_model.py::test_reaction_delete 354s tests/test_core/test_model.py::test_reaction_delete 354s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 354s warn( 354s 354s tests/test_core/test_model.py::test_group_loss_of_elements 354s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 354s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 354s warn("need to pass in a list") 354s 354s tests/test_core/test_model.py::test_change_objective 354s tests/test_core/test_model.py::test_change_objective 354s tests/test_core/test_model.py::test_change_objective 354s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 354s warn("Please use reaction.flux instead.", DeprecationWarning) 354s 354s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 354s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 354s /tmp/autopkgtest.QzeQlX/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 354s assert math.isnan(sol.growth) 354s 354s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 354s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 354s /tmp/autopkgtest.QzeQlX/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 354s assert math.isnan(sol_one.growth) 354s 354s tests/test_io/test_json.py: 1 warning 354s tests/test_io/test_mat.py: 3 warnings 354s tests/test_io/test_pickle.py: 1 warning 354s tests/test_io/test_sbml.py: 9 warnings 354s tests/test_io/test_yaml.py: 1 warning 354s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 354s warn(f"Solver status is '{status}'.", UserWarning) 354s 354s tests/test_io/test_yaml.py::test_save_yaml_model 354s /tmp/autopkgtest.QzeQlX/autopkgtest_tmp/tests/test_io/test_yaml.py:29: PendingDeprecationWarning: 354s you should no longer specify 'unsafe'. 354s For **dumping only** use yaml=YAML(typ='full') 354s 354s yaml = YAML(typ="unsafe") 354s 354s tests/test_medium/test_boundary_types.py: 96 warnings 354s /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]` 354s return most[0] 354s 354s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 354s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 354s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 354s /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]` 354s compartment = most[matches[most]][0] 354s 354s tests/test_util/test_process_pool.py::test_with_context 354s /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 354s self._pool.__enter__() 354s 354s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 354s 354s -------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests --------------------------------------------------------------------------------------------------------------------- 354s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 354s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 354s test_subtract_metabolite_benchmark[cplex] 3.7200 (1.0) 105.7610 (2.56) 3.9186 (1.0) 1.7039 (2.37) 3.8400 (1.0) 0.0800 (1.0) 8;443 255,194.1586 (1.0) 4627 1 354s test_subtract_metabolite_benchmark[glpk] 3.7600 (1.01) 44.7200 (1.08) 3.9922 (1.02) 0.7842 (1.09) 3.9200 (1.02) 0.0810 (1.01) 25;770 250,486.8813 (0.98) 4839 1 354s test_subtract_metabolite_benchmark[gurobi] 3.7600 (1.01) 41.2410 (1.0) 3.9553 (1.01) 0.7197 (1.0) 3.8800 (1.01) 0.0800 (1.0) 23;370 252,823.1289 (0.99) 4840 1 354s test_change_objective_benchmark[optlang-glpk] 188.0820 (50.56) 730.9260 (17.72) 201.7538 (51.49) 17.7569 (24.67) 196.2420 (51.10) 6.4800 (80.99) 410;490 4,956.5365 (0.02) 3798 1 354s test_achr_sample_benchmark 193.3620 (51.98) 470.8850 (11.42) 234.6919 (59.89) 52.7034 (73.23) 212.4420 (55.32) 39.1600 (489.46) 8;7 4,260.9063 (0.02) 62 1 354s test_optgp_sample_benchmark 457.6840 (123.03) 2,075.2590 (50.32) 561.1246 (143.20) 124.1531 (172.51) 531.5250 (138.42) 106.8100 (>1000.0) 55;21 1,782.1354 (0.01) 681 1 354s test_loopless_benchmark_after 1,118.9710 (300.80) 1,419.1730 (34.41) 1,194.9792 (304.95) 58.4164 (81.17) 1,188.7910 (309.58) 84.3600 (>1000.0) 89;6 836.8346 (0.00) 312 1 354s test_loopless_benchmark_before 5,716.1320 (>1000.0) 6,750.1820 (163.68) 5,989.7410 (>1000.0) 153.5723 (213.39) 5,966.1145 (>1000.0) 168.9630 (>1000.0) 17;3 166.9521 (0.00) 82 1 354s test_minimal_medium_linear_benchmark 6,859.7830 (>1000.0) 7,584.8700 (183.92) 7,104.6971 (>1000.0) 141.5101 (196.63) 7,088.4650 (>1000.0) 194.4820 (>1000.0) 22;1 140.7520 (0.00) 86 1 354s test_minimal_medium_mip_benchmark 6,961.9040 (>1000.0) 7,756.1910 (188.07) 7,208.4780 (>1000.0) 159.8363 (222.09) 7,183.9660 (>1000.0) 199.6420 (>1000.0) 22;3 138.7255 (0.00) 86 1 354s test_copy_benchmark[optlang-glpk] 16,354.3880 (>1000.0) 286,510.7590 (>1000.0) 22,241.4948 (>1000.0) 36,304.3036 (>1000.0) 16,854.0330 (>1000.0) 1,516.1832 (>1000.0) 1;1 44.9610 (0.00) 55 1 354s test_single_reaction_deletion_benchmark[glpk] 25,109.6280 (>1000.0) 25,593.3130 (620.58) 25,329.9424 (>1000.0) 125.1337 (173.87) 25,308.3900 (>1000.0) 217.1420 (>1000.0) 16;0 39.4790 (0.00) 36 1 354s test_deepcopy_benchmark 25,577.4720 (>1000.0) 444,109.9110 (>1000.0) 37,874.4647 (>1000.0) 66,768.5618 (>1000.0) 27,273.6070 (>1000.0) 2,022.7085 (>1000.0) 1;1 26.4030 (0.00) 39 1 354s test_gpr_equality_benchmark 26,047.5160 (>1000.0) 30,175.3530 (731.68) 27,048.5411 (>1000.0) 748.4337 (>1000.0) 26,989.5250 (>1000.0) 874.6180 (>1000.0) 5;1 36.9706 (0.00) 33 1 354s test_fastcc_benchmark[glpk] 58,583.3320 (>1000.0) 264,522.6050 (>1000.0) 74,658.6111 (>1000.0) 50,676.1413 (>1000.0) 61,698.7810 (>1000.0) 4,062.6370 (>1000.0) 1;1 13.3943 (0.00) 16 1 354s test_add_metabolite_benchmark[gurobi] 64,762.5070 (>1000.0) 65,990.3980 (>1000.0) 65,437.5803 (>1000.0) 380.6066 (528.85) 65,488.1530 (>1000.0) 667.2065 (>1000.0) 6;0 15.2817 (0.00) 16 1 354s test_add_metabolite_benchmark[glpk] 64,923.7080 (>1000.0) 68,071.4570 (>1000.0) 66,156.5640 (>1000.0) 914.5647 (>1000.0) 65,960.2970 (>1000.0) 1,142.9095 (>1000.0) 5;0 15.1157 (0.00) 16 1 354s test_add_metabolite_benchmark[cplex] 66,102.7980 (>1000.0) 78,412.3910 (>1000.0) 67,864.3570 (>1000.0) 3,050.7573 (>1000.0) 66,777.9245 (>1000.0) 1,138.4905 (>1000.0) 2;2 14.7353 (0.00) 16 1 354s test_single_gene_deletion_fba_benchmark[glpk] 82,355.8680 (>1000.0) 93,936.0130 (>1000.0) 86,711.3596 (>1000.0) 3,596.2903 (>1000.0) 86,205.4430 (>1000.0) 4,283.3990 (>1000.0) 3;0 11.5325 (0.00) 10 1 354s test_achr_init_benchmark 97,007.4870 (>1000.0) 104,332.6340 (>1000.0) 99,179.6867 (>1000.0) 2,169.8543 (>1000.0) 98,820.3235 (>1000.0) 2,497.7030 (>1000.0) 2;1 10.0827 (0.00) 10 1 354s test_optgp_init_benchmark 110,735.8120 (>1000.0) 119,977.0570 (>1000.0) 114,677.6042 (>1000.0) 3,275.6695 (>1000.0) 114,503.0470 (>1000.0) 5,278.1790 (>1000.0) 3;0 8.7201 (0.00) 9 1 354s test_flux_variability_loopless_benchmark[glpk] 121,410.3860 (>1000.0) 152,162.5060 (>1000.0) 130,711.1854 (>1000.0) 10,244.6932 (>1000.0) 127,657.0225 (>1000.0) 11,535.3850 (>1000.0) 1;0 7.6505 (0.00) 8 1 354s test_gpr_symbolism_benchmark 175,631.3930 (>1000.0) 182,529.0150 (>1000.0) 178,972.8386 (>1000.0) 2,710.4209 (>1000.0) 178,960.6620 (>1000.0) 4,223.8787 (>1000.0) 2;0 5.5874 (0.00) 5 1 354s test_single_gene_deletion_linear_moma_benchmark[glpk] 178,688.7830 (>1000.0) 181,820.7710 (>1000.0) 180,037.1752 (>1000.0) 1,082.6574 (>1000.0) 179,748.1725 (>1000.0) 1,156.2100 (>1000.0) 2;0 5.5544 (0.00) 6 1 354s test_single_gene_deletion_linear_room_benchmark[glpk] 269,267.6460 (>1000.0) 587,486.0180 (>1000.0) 335,749.6266 (>1000.0) 140,745.2367 (>1000.0) 273,772.0870 (>1000.0) 82,155.5270 (>1000.0) 1;1 2.9784 (0.00) 5 1 354s test_double_gene_deletion_benchmark 277,739.8900 (>1000.0) 291,935.8200 (>1000.0) 283,432.0222 (>1000.0) 5,491.4526 (>1000.0) 283,796.6250 (>1000.0) 7,023.6740 (>1000.0) 2;0 3.5282 (0.00) 5 1 354s test_pfba_benchmark[glpk] 290,629.4440 (>1000.0) 301,001.9380 (>1000.0) 294,119.0116 (>1000.0) 4,133.1123 (>1000.0) 292,258.0980 (>1000.0) 4,751.6430 (>1000.0) 1;0 3.4000 (0.00) 5 1 354s test_copy_benchmark_large_model[optlang-glpk] 327,988.7760 (>1000.0) 689,862.2620 (>1000.0) 466,284.0396 (>1000.0) 187,146.6949 (>1000.0) 332,177.4540 (>1000.0) 331,885.1830 (>1000.0) 1;0 2.1446 (0.00) 5 1 354s test_double_reaction_deletion_benchmark 376,909.7940 (>1000.0) 494,151.9030 (>1000.0) 464,767.9396 (>1000.0) 49,323.6921 (>1000.0) 485,014.3010 (>1000.0) 32,354.6557 (>1000.0) 1;1 2.1516 (0.00) 5 1 354s test_geometric_fba_benchmark[glpk] 401,609.4120 (>1000.0) 407,080.1810 (>1000.0) 404,965.6500 (>1000.0) 2,089.7687 (>1000.0) 405,429.1260 (>1000.0) 2,536.9835 (>1000.0) 2;0 2.4693 (0.00) 5 1 354s test_flux_variability_benchmark[glpk] 490,086.5820 (>1000.0) 497,044.7650 (>1000.0) 494,233.0672 (>1000.0) 2,859.5222 (>1000.0) 494,774.9050 (>1000.0) 4,545.8913 (>1000.0) 1;0 2.0233 (0.00) 5 1 354s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 354s 354s Legend: 354s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 354s OPS: Operations Per Second, computed as 1 / Mean 354s = 509 passed, 31 skipped, 10 xfailed, 1 xpassed, 170 warnings in 103.73s (0:01:43) = 356s Removing patch debian/patches/no_future_dependency.patch 356s Restoring setup.cfg 356s 356s Removing patch debian/patches/32-bit-test.patch 356s Restoring tests/test_io/test_mat.py 356s 356s Removing patch debian/patches/do-not-seek-for-name.patch 356s Restoring src/cobra/io/sbml.py 356s 356s Removing patch debian/patches/ignore_tests.patch 356s Restoring tests/test_io/test_web/test_load.py 356s 357s Removing patch debian/patches/xfail_test_show_versions.patch 357s Restoring tests/test_util/test_util.py 357s 357s Removing patch debian/patches/mathjax.patch 357s Restoring documentation_builder/conf.py 357s 357s No patches applied 357s PASS 357s autopkgtest [20:04:37]: test run-unit-test: -----------------------] 361s autopkgtest [20:04:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 361s run-unit-test PASS 364s autopkgtest [20:04:44]: @@@@@@@@@@@@@@@@@@@@ summary 364s run-unit-test PASS