0s autopkgtest [21:16:46]: starting date and time: 2024-05-03 21:16:46+0000 0s autopkgtest [21:16:46]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [21:16:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wl5ejxj_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:httpx --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=httpx/0.27.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-8.secgroup --name adt-oracular-arm64-python-cobra-20240503-211646-juju-7f2275-prod-proposed-migration-environment-2-54162f37-3ab9-4c8b-af68-e01c174d37b9 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 375s autopkgtest [21:23:01]: testbed dpkg architecture: arm64 375s autopkgtest [21:23:01]: testbed apt version: 2.7.14build2 375s autopkgtest [21:23:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 376s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 377s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [35.7 kB] 377s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [2016 kB] 377s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 377s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [150 kB] 377s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [213 kB] 377s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [13.1 kB] 377s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [1393 kB] 378s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [27.5 kB] 378s Fetched 3916 kB in 2s (2254 kB/s) 378s Reading package lists... 382s Reading package lists... 383s Building dependency tree... 383s Reading state information... 384s Calculating upgrade... 385s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 385s Reading package lists... 385s Building dependency tree... 385s Reading state information... 387s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 387s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 387s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 387s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 387s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 390s Reading package lists... 390s Reading package lists... 390s Building dependency tree... 390s Reading state information... 391s Calculating upgrade... 392s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 392s Reading package lists... 393s Building dependency tree... 393s Reading state information... 394s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 397s autopkgtest [21:23:23]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 398s autopkgtest [21:23:24]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 401s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 401s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 401s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 401s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 401s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 401s gpgv: Can't check signature: No public key 401s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 402s autopkgtest [21:23:28]: testing package python-cobra version 0.29.0-1ubuntu2 402s autopkgtest [21:23:28]: build not needed 403s autopkgtest [21:23:29]: test run-unit-test: preparing testbed 405s Reading package lists... 405s Building dependency tree... 405s Reading state information... 406s Starting pkgProblemResolver with broken count: 0 406s Starting 2 pkgProblemResolver with broken count: 0 406s Done 407s The following additional packages will be installed: 407s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 407s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 407s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 407s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 407s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 407s python3-importlib-resources python3-iniconfig python3-more-itertools 407s python3-mpmath python3-numpy python3-optlang python3-packaging 407s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 407s python3-pytest python3-pytest-benchmark python3-pytest-mock 407s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 407s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 407s python3-tabulate python3-zipp quilt swig 407s Suggested packages: 407s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 407s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 407s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 407s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 407s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 407s swig-doc swig-examples 407s Recommended packages: 407s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 407s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 407s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 407s python3-pil isympy-common 408s The following NEW packages will be installed: 408s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 408s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 408s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 408s python3-click python3-cobra python3-colorama python3-cpuinfo 408s python3-dateutil python3-decorator python3-depinfo python3-diskcache 408s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 408s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 408s python3-optlang python3-packaging python3-pandas python3-pandas-lib 408s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 408s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 408s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 408s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 408s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 408s Need to get 47.8 MB/47.8 MB of archives. 408s After this operation, 230 MB of additional disk space will be used. 408s Get:1 /tmp/autopkgtest.XaftUD/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [772 B] 408s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 diffstat arm64 1.66-1build1 [28.1 kB] 408s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] 408s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 gettext arm64 0.21-14ubuntu2 [845 kB] 408s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 libsuitesparseconfig7 arm64 1:7.6.1+dfsg-1build1 [12.5 kB] 408s Get:6 http://ftpmaster.internal/ubuntu oracular/universe arm64 libamd3 arm64 1:7.6.1+dfsg-1build1 [25.7 kB] 408s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 408s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libcolamd3 arm64 1:7.6.1+dfsg-1build1 [18.1 kB] 408s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14-20240412-0ubuntu1 [444 kB] 408s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 408s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 408s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 409s Get:13 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 409s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libpython3.12t64 arm64 3.12.3-1 [2278 kB] 409s Get:15 http://ftpmaster.internal/ubuntu oracular/universe arm64 python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 409s Get:16 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sniffio all 1.3.0-2 [7216 B] 409s Get:17 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-anyio all 4.2.0-1 [56.5 kB] 409s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 409s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 409s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-click all 8.1.6-2 [79.0 kB] 409s Get:21 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-depinfo arm64 2.2.0-2 [10.9 kB] 409s Get:22 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-diskcache all 5.4.0-3 [34.6 kB] 409s Get:23 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h11 all 0.14.0-1 [51.1 kB] 409s Get:24 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-httpcore all 1.0.2-2 [38.3 kB] 409s Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-httpx all 0.27.0-1 [60.9 kB] 409s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 409s Get:27 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-zipp all 1.0.0-6 [6090 B] 409s Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-importlib-resources all 6.0.1-1 [22.1 kB] 409s Get:29 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-6ubuntu1 [3565 kB] 410s Get:30 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-swiglpk arm64 5.0.10-1build1 [71.9 kB] 410s Get:31 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 410s Get:32 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sympy all 1.12-7 [3966 kB] 410s Get:33 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-optlang all 1.8.1-1 [82.7 kB] 410s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 410s Get:35 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-7 [4178 kB] 410s Get:36 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas all 2.1.4+dfsg-7 [3042 kB] 410s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pydantic arm64 1.10.14-1 [1688 kB] 410s Get:38 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8-1build1 [126 kB] 410s Get:39 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 410s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-simplejson arm64 3.19.2-1build2 [53.6 kB] 410s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB] 410s Get:42 http://ftpmaster.internal/ubuntu oracular/universe arm64 swig arm64 4.2.0-2ubuntu1 [1152 kB] 410s Get:43 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sbml5 arm64 5.20.2+dfsg-3 [3539 kB] 410s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cobra arm64 0.29.0-1ubuntu2 [1119 kB] 411s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cpuinfo all 9.0.0-1 [21.2 kB] 411s Get:46 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 411s Get:47 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 411s Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 411s Get:49 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 411s Get:50 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 411s Get:51 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 411s Get:52 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 411s Get:53 http://ftpmaster.internal/ubuntu oracular/universe arm64 quilt all 0.67+really0.67-4 [436 kB] 411s Get:54 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.11.4-6build1 [15.0 MB] 412s Fetched 47.8 MB in 3s (13.9 MB/s) 412s Selecting previously unselected package diffstat. 412s (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 ... 77894 files and directories currently installed.) 412s Preparing to unpack .../00-diffstat_1.66-1build1_arm64.deb ... 412s Unpacking diffstat (1.66-1build1) ... 412s Selecting previously unselected package libgomp1:arm64. 412s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_arm64.deb ... 412s Unpacking libgomp1:arm64 (14-20240412-0ubuntu1) ... 412s Selecting previously unselected package gettext. 412s Preparing to unpack .../02-gettext_0.21-14ubuntu2_arm64.deb ... 412s Unpacking gettext (0.21-14ubuntu2) ... 412s Selecting previously unselected package libsuitesparseconfig7:arm64. 412s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_arm64.deb ... 412s Unpacking libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 412s Selecting previously unselected package libamd3:arm64. 412s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_arm64.deb ... 412s Unpacking libamd3:arm64 (1:7.6.1+dfsg-1build1) ... 412s Selecting previously unselected package libblas3:arm64. 412s Preparing to unpack .../05-libblas3_3.12.0-3build1_arm64.deb ... 412s Unpacking libblas3:arm64 (3.12.0-3build1) ... 412s Selecting previously unselected package libcolamd3:arm64. 412s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_arm64.deb ... 412s Unpacking libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 413s Selecting previously unselected package libgfortran5:arm64. 413s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_arm64.deb ... 413s Unpacking libgfortran5:arm64 (14-20240412-0ubuntu1) ... 413s Selecting previously unselected package libltdl7:arm64. 413s Preparing to unpack .../08-libltdl7_2.4.7-7build1_arm64.deb ... 413s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 413s Selecting previously unselected package libglpk40:arm64. 413s Preparing to unpack .../09-libglpk40_5.0-1build2_arm64.deb ... 413s Unpacking libglpk40:arm64 (5.0-1build2) ... 413s Selecting previously unselected package liblapack3:arm64. 413s Preparing to unpack .../10-liblapack3_3.12.0-3build1_arm64.deb ... 413s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 413s Selecting previously unselected package liblbfgsb0:arm64. 413s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 413s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 413s Selecting previously unselected package libpython3.12t64:arm64. 413s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_arm64.deb ... 413s Unpacking libpython3.12t64:arm64 (3.12.3-1) ... 413s Selecting previously unselected package python-cobra-data. 413s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 413s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 413s Selecting previously unselected package python3-sniffio. 413s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 413s Unpacking python3-sniffio (1.3.0-2) ... 413s Selecting previously unselected package python3-anyio. 413s Preparing to unpack .../15-python3-anyio_4.2.0-1_all.deb ... 413s Unpacking python3-anyio (4.2.0-1) ... 413s Selecting previously unselected package python3-appdirs. 413s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 413s Unpacking python3-appdirs (1.4.4-4) ... 413s Selecting previously unselected package python3-colorama. 413s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 413s Unpacking python3-colorama (0.4.6-4) ... 414s Selecting previously unselected package python3-click. 414s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 414s Unpacking python3-click (8.1.6-2) ... 414s Selecting previously unselected package python3-depinfo. 414s Preparing to unpack .../19-python3-depinfo_2.2.0-2_arm64.deb ... 414s Unpacking python3-depinfo (2.2.0-2) ... 414s Selecting previously unselected package python3-diskcache. 414s Preparing to unpack .../20-python3-diskcache_5.4.0-3_all.deb ... 414s Unpacking python3-diskcache (5.4.0-3) ... 414s Selecting previously unselected package python3-h11. 414s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 414s Unpacking python3-h11 (0.14.0-1) ... 414s Selecting previously unselected package python3-httpcore. 414s Preparing to unpack .../22-python3-httpcore_1.0.2-2_all.deb ... 414s Unpacking python3-httpcore (1.0.2-2) ... 414s Selecting previously unselected package python3-httpx. 414s Preparing to unpack .../23-python3-httpx_0.27.0-1_all.deb ... 414s Unpacking python3-httpx (0.27.0-1) ... 414s Selecting previously unselected package python3-more-itertools. 414s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 414s Unpacking python3-more-itertools (10.2.0-1) ... 414s Selecting previously unselected package python3-zipp. 414s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 414s Unpacking python3-zipp (1.0.0-6) ... 414s Selecting previously unselected package python3-importlib-resources. 414s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 414s Unpacking python3-importlib-resources (6.0.1-1) ... 414s Selecting previously unselected package python3-numpy. 414s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_arm64.deb ... 414s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 414s Selecting previously unselected package python3-swiglpk. 415s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_arm64.deb ... 415s Unpacking python3-swiglpk (5.0.10-1build1) ... 415s Selecting previously unselected package python3-mpmath. 415s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 415s Unpacking python3-mpmath (1.2.1-3) ... 415s Selecting previously unselected package python3-sympy. 415s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 415s Unpacking python3-sympy (1.12-7) ... 415s Selecting previously unselected package python3-optlang. 415s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 415s Unpacking python3-optlang (1.8.1-1) ... 416s Selecting previously unselected package python3-dateutil. 416s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 416s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 416s Selecting previously unselected package python3-pandas-lib:arm64. 416s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_arm64.deb ... 416s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-7) ... 416s Selecting previously unselected package python3-pandas. 416s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 416s Unpacking python3-pandas (2.1.4+dfsg-7) ... 417s Selecting previously unselected package python3-pydantic. 417s Preparing to unpack .../35-python3-pydantic_1.10.14-1_arm64.deb ... 417s Unpacking python3-pydantic (1.10.14-1) ... 417s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 417s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8-1build1_arm64.deb ... 417s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8-1build1) ... 417s Selecting previously unselected package python3-ruamel.yaml. 417s Preparing to unpack .../37-python3-ruamel.yaml_0.17.21-1_all.deb ... 417s Unpacking python3-ruamel.yaml (0.17.21-1) ... 417s Selecting previously unselected package python3-simplejson. 417s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_arm64.deb ... 417s Unpacking python3-simplejson (3.19.2-1build2) ... 417s Selecting previously unselected package python3-tabulate. 417s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 417s Unpacking python3-tabulate (0.8.10-1) ... 417s Selecting previously unselected package swig. 417s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_arm64.deb ... 417s Unpacking swig (4.2.0-2ubuntu1) ... 417s Selecting previously unselected package python3-sbml5. 417s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_arm64.deb ... 417s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 418s Selecting previously unselected package python3-cobra. 418s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_arm64.deb ... 418s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 418s Selecting previously unselected package python3-cpuinfo. 418s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 418s Unpacking python3-cpuinfo (9.0.0-1) ... 418s Selecting previously unselected package python3-decorator. 418s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 418s Unpacking python3-decorator (5.1.1-5) ... 418s Selecting previously unselected package python3-iniconfig. 418s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 418s Unpacking python3-iniconfig (1.1.1-2) ... 418s Selecting previously unselected package python3-packaging. 418s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 418s Unpacking python3-packaging (24.0-1) ... 418s Selecting previously unselected package python3-pluggy. 418s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 418s Unpacking python3-pluggy (1.4.0-1) ... 418s Selecting previously unselected package python3-pytest. 418s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 418s Unpacking python3-pytest (7.4.4-1) ... 418s Selecting previously unselected package python3-pytest-benchmark. 418s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 418s Unpacking python3-pytest-benchmark (4.0.0-3) ... 418s Selecting previously unselected package python3-pytest-mock. 418s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 418s Unpacking python3-pytest-mock (3.12.0-1.1) ... 418s Selecting previously unselected package quilt. 418s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 418s Unpacking quilt (0.67+really0.67-4) ... 418s Selecting previously unselected package python3-scipy. 418s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_arm64.deb ... 418s Unpacking python3-scipy (1.11.4-6build1) ... 419s Selecting previously unselected package autopkgtest-satdep. 419s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 419s Unpacking autopkgtest-satdep (0) ... 419s Setting up python3-more-itertools (10.2.0-1) ... 420s Setting up python3-iniconfig (1.1.1-2) ... 420s Setting up python3-sniffio (1.3.0-2) ... 421s Setting up swig (4.2.0-2ubuntu1) ... 421s Setting up python3-anyio (4.2.0-1) ... 421s Setting up python3-colorama (0.4.6-4) ... 421s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8-1build1) ... 421s Setting up python3-tabulate (0.8.10-1) ... 422s Setting up python3-zipp (1.0.0-6) ... 422s Setting up libgomp1:arm64 (14-20240412-0ubuntu1) ... 422s Setting up python3-click (8.1.6-2) ... 423s Setting up libpython3.12t64:arm64 (3.12.3-1) ... 423s Setting up python3-simplejson (3.19.2-1build2) ... 423s Setting up python3-decorator (5.1.1-5) ... 423s Setting up libblas3:arm64 (3.12.0-3build1) ... 423s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 423s Setting up python3-packaging (24.0-1) ... 424s Setting up python3-pydantic (1.10.14-1) ... 424s Setting up diffstat (1.66-1build1) ... 424s Setting up python3-h11 (0.14.0-1) ... 425s Setting up python3-depinfo (2.2.0-2) ... 425s Setting up python3-cpuinfo (9.0.0-1) ... 426s Setting up libltdl7:arm64 (2.4.7-7build1) ... 426s Setting up libgfortran5:arm64 (14-20240412-0ubuntu1) ... 426s Setting up python3-pluggy (1.4.0-1) ... 426s Setting up python3-ruamel.yaml (0.17.21-1) ... 427s Setting up libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 427s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 427s Setting up python3-mpmath (1.2.1-3) ... 428s Setting up python3-diskcache (5.4.0-3) ... 429s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 429s Setting up python3-appdirs (1.4.4-4) ... 429s Setting up python3-httpcore (1.0.2-2) ... 430s Setting up python3-sympy (1.12-7) ... 444s Setting up liblapack3:arm64 (3.12.0-3build1) ... 444s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 444s Setting up gettext (0.21-14ubuntu2) ... 444s Setting up libamd3:arm64 (1:7.6.1+dfsg-1build1) ... 444s Setting up python3-importlib-resources (6.0.1-1) ... 444s Setting up libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 444s Setting up python3-pytest (7.4.4-1) ... 445s Setting up quilt (0.67+really0.67-4) ... 445s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 446s Setting up python3-httpx (0.27.0-1) ... 446s Setting up libglpk40:arm64 (5.0-1build2) ... 446s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 451s Setting up python3-pytest-mock (3.12.0-1.1) ... 451s Setting up python3-swiglpk (5.0.10-1build1) ... 452s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 452s Setting up python3-optlang (1.8.1-1) ... 452s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 452s """A representation of the convex optimizatgion problem in standard form. 452s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 452s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 452s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 452s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 452s Setting up python3-pytest-benchmark (4.0.0-3) ... 453s Setting up python3-scipy (1.11.4-6build1) ... 460s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-7) ... 460s Setting up python3-pandas (2.1.4+dfsg-7) ... 471s Setting up python3-cobra (0.29.0-1ubuntu2) ... 472s Setting up autopkgtest-satdep (0) ... 472s Processing triggers for man-db (2.12.0-4build2) ... 472s Processing triggers for install-info (7.1-3build2) ... 473s Processing triggers for libc-bin (2.39-0ubuntu8) ... 480s (Reading database ... 85904 files and directories currently installed.) 480s Removing autopkgtest-satdep (0) ... 481s autopkgtest [21:24:47]: test run-unit-test: [----------------------- 481s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 481s Running Tests 481s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 489s ============================= test session starts ============================== 489s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 489s 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) 489s rootdir: /tmp/autopkgtest.XaftUD/autopkgtest_tmp 489s plugins: mock-3.12.0, benchmark-4.0.0, anyio-4.2.0 489s collected 551 items 489s 490s tests/test_core/test_configuration.py ...... [ 1%] 497s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 499s ...................x....... [ 12%] 499s tests/test_core/test_dictlist.py ...................... [ 16%] 499s tests/test_core/test_formula.py ..... [ 17%] 499s tests/test_core/test_gene.py . [ 17%] 500s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 524s .......................... [ 29%] 524s tests/test_core/test_group.py .. [ 30%] 525s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 545s tests/test_core/test_model.py .......................................... [ 39%] 547s ...........s..s.ss. [ 43%] 547s tests/test_core/test_solution.py .ss [ 43%] 560s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 562s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 570s tests/test_flux_analysis/test_geometric.py .. [ 46%] 572s tests/test_flux_analysis/test_moma.py . [ 46%] 582s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 582s tests/test_flux_analysis/test_reaction.py . [ 47%] 589s tests/test_flux_analysis/test_room.py .... [ 47%] 603s tests/test_flux_analysis/test_variability.py ....... [ 49%] 603s tests/test_flux_analysis/test_deletion.py sss [ 49%] 603s tests/test_flux_analysis/test_moma.py s [ 49%] 618s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 626s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 626s tests/test_flux_analysis/test_helpers.py ... [ 51%] 627s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 635s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 636s tests/test_flux_analysis/test_variability.py ....... [ 54%] 636s tests/test_io/test_annotation.py .. [ 55%] 636s tests/test_io/test_annotation_format.py .. [ 55%] 645s tests/test_io/test_io_order.py ........................... [ 60%] 645s tests/test_io/test_json.py .... [ 61%] 698s tests/test_io/test_mat.py ............... [ 64%] 698s tests/test_io/test_notes.py . [ 64%] 698s tests/test_io/test_pickle.py .. [ 64%] 714s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 715s tests/test_io/test_yaml.py .x [ 72%] 716s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 716s tests/test_manipulation/test_annotate.py . [ 73%] 719s tests/test_manipulation/test_delete.py ....... [ 75%] 719s tests/test_manipulation/test_modify.py ... [ 75%] 719s tests/test_manipulation/test_validate.py .. [ 76%] 720s tests/test_medium/test_boundary_types.py ......... [ 77%] 722s tests/test_medium/test_minimal_medium.py .......... [ 79%] 726s tests/test_sampling/test_achr.py ...... [ 80%] 731s tests/test_sampling/test_optgp.py ...... [ 81%] 749s tests/test_sampling/test_sampling.py .......... [ 83%] 754s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 758s tests/test_summary/test_model_summary.py ............... [ 89%] 761s tests/test_summary/test_reaction_summary.py .................... [ 92%] 761s tests/test_util/test_array.py .. [ 93%] 761s tests/test_util/test_context.py ... [ 93%] 764s tests/test_util/test_process_pool.py ............... [ 96%] 767s tests/test_util/test_solver.py ..............s [ 99%] 767s tests/test_util/test_util.py ...X [100%] 767s 767s =============================== warnings summary =============================== 767s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 767s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 767s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 767s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 767s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 767s /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)'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 767s warn( 767s 767s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 767s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 767s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 767s warn( 767s 767s tests/test_core/test_model.py::test_reaction_delete 767s tests/test_core/test_model.py::test_reaction_delete 767s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 767s warn( 767s 767s tests/test_core/test_model.py::test_group_loss_of_elements 767s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 767s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 767s warn("need to pass in a list") 767s 767s tests/test_core/test_model.py::test_change_objective 767s tests/test_core/test_model.py::test_change_objective 767s tests/test_core/test_model.py::test_change_objective 767s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 767s warn("Please use reaction.flux instead.", DeprecationWarning) 767s 767s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 767s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 767s /tmp/autopkgtest.XaftUD/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 767s assert math.isnan(sol.growth) 767s 767s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 767s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 767s /tmp/autopkgtest.XaftUD/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 767s assert math.isnan(sol_one.growth) 767s 767s tests/test_io/test_json.py: 1 warning 767s tests/test_io/test_mat.py: 5 warnings 767s tests/test_io/test_pickle.py: 1 warning 767s tests/test_io/test_sbml.py: 9 warnings 767s tests/test_io/test_yaml.py: 1 warning 767s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 767s warn(f"Solver status is '{status}'.", UserWarning) 767s 767s tests/test_medium/test_boundary_types.py: 96 warnings 767s /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]` 767s return most[0] 767s 767s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 767s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 767s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 767s /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]` 767s compartment = most[matches[most]][0] 767s 767s tests/test_util/test_process_pool.py::test_with_context 767s /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 767s self._pool.__enter__() 767s 767s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 767s 767s ------------------------------------------------------------------------------------------------------------------------ benchmark: 31 tests ------------------------------------------------------------------------------------------------------------------------- 767s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 767s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 767s test_subtract_metabolite_benchmark[cplex] 8.8500 (1.0) 80.7010 (1.0) 9.7976 (1.0) 3.3342 (1.0) 9.1500 (1.0) 0.2500 (1.0) 101;181 102,065.5002 (1.0) 1851 1 767s test_subtract_metabolite_benchmark[gurobi] 8.8750 (1.00) 84.3260 (1.04) 10.0121 (1.02) 4.2875 (1.29) 9.2750 (1.01) 0.3250 (1.30) 79;173 99,879.6224 (0.98) 1894 1 767s test_subtract_metabolite_benchmark[glpk] 8.9010 (1.01) 116.5020 (1.44) 11.4603 (1.17) 5.4710 (1.64) 9.6500 (1.05) 3.0690 (12.28) 73;73 87,257.4365 (0.85) 1767 1 767s test_achr_sample_benchmark 608.6180 (68.77) 902.9150 (11.19) 655.7350 (66.93) 35.8075 (10.74) 652.3420 (71.29) 38.9875 (155.95) 115;15 1,525.0062 (0.01) 351 1 767s test_change_objective_benchmark[optlang-glpk] 612.5920 (69.22) 1,719.3800 (21.31) 670.1119 (68.40) 52.1720 (15.65) 661.8670 (72.34) 37.1000 (148.40) 209;133 1,492.2882 (0.01) 1827 1 767s test_optgp_sample_benchmark 948.3390 (107.16) 1,254.1610 (15.54) 1,015.0073 (103.60) 42.1340 (12.64) 997.9890 (109.07) 52.6740 (210.70) 107;19 985.2146 (0.01) 642 1 767s test_loopless_benchmark_after 2,807.0200 (317.18) 3,697.6520 (45.82) 3,020.4936 (308.29) 166.8134 (50.03) 2,973.5220 (324.98) 122.6187 (490.47) 16;10 331.0717 (0.00) 143 1 767s test_single_gene_deletion_fba_benchmark[glpk] 10,434.7420 (>1000.0) 12,527.3900 (155.23) 10,891.1286 (>1000.0) 379.2585 (113.75) 10,779.6630 (>1000.0) 287.2402 (>1000.0) 14;7 91.8178 (0.00) 75 1 767s test_loopless_benchmark_before 14,980.4900 (>1000.0) 18,619.7190 (230.72) 16,066.8405 (>1000.0) 1,232.0465 (369.52) 15,367.9690 (>1000.0) 1,623.8048 (>1000.0) 8;0 62.2400 (0.00) 43 1 767s test_minimal_medium_mip_benchmark 16,809.2490 (>1000.0) 19,287.9990 (239.01) 17,741.8632 (>1000.0) 520.3730 (156.07) 17,681.6150 (>1000.0) 558.0812 (>1000.0) 7;2 56.3639 (0.00) 37 1 767s test_minimal_medium_linear_benchmark 17,244.1960 (>1000.0) 19,381.9500 (240.17) 17,963.1368 (>1000.0) 447.9573 (134.35) 17,933.8880 (>1000.0) 554.9700 (>1000.0) 12;1 55.6696 (0.00) 38 1 767s test_copy_benchmark[optlang-glpk] 43,392.2410 (>1000.0) 54,716.1480 (678.01) 47,541.9070 (>1000.0) 3,142.4871 (942.51) 46,914.9810 (>1000.0) 5,313.0072 (>1000.0) 7;0 21.0341 (0.00) 21 1 767s test_flux_variability_loopless_benchmark[glpk] 59,045.0980 (>1000.0) 70,439.8470 (872.85) 61,789.9681 (>1000.0) 3,708.9898 (>1000.0) 60,379.4120 (>1000.0) 2,364.7200 (>1000.0) 1;1 16.1839 (0.00) 8 1 767s test_single_reaction_deletion_benchmark[glpk] 66,269.3520 (>1000.0) 80,940.6620 (>1000.0) 69,904.8899 (>1000.0) 5,089.7352 (>1000.0) 67,749.2050 (>1000.0) 970.2468 (>1000.0) 3;3 14.3052 (0.00) 15 1 767s test_deepcopy_benchmark 67,581.6910 (>1000.0) 79,001.9550 (978.95) 74,103.1929 (>1000.0) 3,305.8752 (991.52) 74,347.9145 (>1000.0) 4,580.6490 (>1000.0) 5;0 13.4947 (0.00) 14 1 767s test_gpr_equality_benchmark 71,864.8470 (>1000.0) 84,051.4780 (>1000.0) 74,690.2321 (>1000.0) 3,561.5619 (>1000.0) 73,354.8495 (>1000.0) 2,652.2670 (>1000.0) 2;1 13.3886 (0.00) 12 1 767s test_add_metabolite_benchmark[cplex] 166,482.0270 (>1000.0) 185,955.8960 (>1000.0) 172,038.1534 (>1000.0) 8,350.3374 (>1000.0) 167,285.0900 (>1000.0) 11,874.8807 (>1000.0) 2;0 5.8127 (0.00) 7 1 767s test_add_metabolite_benchmark[glpk] 169,405.4740 (>1000.0) 173,669.4510 (>1000.0) 171,396.7779 (>1000.0) 1,473.3513 (441.90) 171,249.3370 (>1000.0) 2,073.9597 (>1000.0) 2;0 5.8344 (0.00) 7 1 767s test_fastcc_benchmark[glpk] 171,757.6340 (>1000.0) 182,744.7200 (>1000.0) 176,680.2817 (>1000.0) 4,442.7433 (>1000.0) 176,437.5180 (>1000.0) 8,582.3480 (>1000.0) 3;0 5.6599 (0.00) 6 1 767s test_add_metabolite_benchmark[gurobi] 202,445.1790 (>1000.0) 233,107.5430 (>1000.0) 216,612.9732 (>1000.0) 12,019.3265 (>1000.0) 217,880.8960 (>1000.0) 18,111.4005 (>1000.0) 2;0 4.6165 (0.00) 5 1 767s test_optgp_init_benchmark 232,012.6850 (>1000.0) 1,584,018.0940 (>1000.0) 505,281.1508 (>1000.0) 603,041.4622 (>1000.0) 238,153.6410 (>1000.0) 343,237.2492 (>1000.0) 1;1 1.9791 (0.00) 5 1 767s test_achr_init_benchmark 232,466.9100 (>1000.0) 243,037.4030 (>1000.0) 237,610.5392 (>1000.0) 3,870.7163 (>1000.0) 237,191.4090 (>1000.0) 4,720.3003 (>1000.0) 2;0 4.2086 (0.00) 5 1 767s test_double_reaction_deletion_benchmark 265,789.9210 (>1000.0) 267,133.4410 (>1000.0) 266,387.9422 (>1000.0) 614.1429 (184.20) 266,212.7870 (>1000.0) 1,132.5945 (>1000.0) 1;0 3.7539 (0.00) 5 1 767s test_single_gene_deletion_linear_moma_benchmark[glpk] 499,668.5660 (>1000.0) 514,063.5650 (>1000.0) 504,900.0730 (>1000.0) 5,824.6234 (>1000.0) 504,159.4880 (>1000.0) 8,188.5682 (>1000.0) 1;0 1.9806 (0.00) 5 1 767s test_gpr_symbolism_benchmark 563,001.6540 (>1000.0) 575,516.1210 (>1000.0) 570,209.7258 (>1000.0) 5,410.9933 (>1000.0) 570,843.3410 (>1000.0) 9,474.5040 (>1000.0) 1;0 1.7537 (0.00) 5 1 767s test_single_gene_deletion_linear_room_benchmark[glpk] 740,505.3820 (>1000.0) 761,726.1790 (>1000.0) 753,156.9218 (>1000.0) 8,072.8183 (>1000.0) 755,239.4480 (>1000.0) 10,148.5417 (>1000.0) 2;0 1.3277 (0.00) 5 1 767s test_pfba_benchmark[glpk] 751,688.0030 (>1000.0) 1,355,216.2150 (>1000.0) 879,081.0356 (>1000.0) 266,428.6494 (>1000.0) 754,496.8030 (>1000.0) 170,967.2353 (>1000.0) 1;1 1.1376 (0.00) 5 1 767s test_double_gene_deletion_benchmark 772,723.4370 (>1000.0) 815,324.5310 (>1000.0) 795,985.8162 (>1000.0) 19,164.0776 (>1000.0) 794,143.4590 (>1000.0) 35,158.3070 (>1000.0) 3;0 1.2563 (0.00) 5 1 767s test_copy_benchmark_large_model[optlang-glpk] 952,686.9790 (>1000.0) 1,981,783.0610 (>1000.0) 1,340,436.5506 (>1000.0) 504,339.6515 (>1000.0) 993,854.7660 (>1000.0) 867,791.3747 (>1000.0) 1;0 0.7460 (0.00) 5 1 767s test_geometric_fba_benchmark[glpk] 1,066,563.9230 (>1000.0) 1,145,963.0340 (>1000.0) 1,088,523.0826 (>1000.0) 32,506.6824 (>1000.0) 1,075,437.7000 (>1000.0) 24,956.4453 (>1000.0) 1;1 0.9187 (0.00) 5 1 767s test_flux_variability_benchmark[glpk] 1,416,033.9980 (>1000.0) 1,451,842.6900 (>1000.0) 1,436,427.2188 (>1000.0) 13,256.5310 (>1000.0) 1,439,169.0440 (>1000.0) 15,610.2950 (>1000.0) 2;0 0.6962 (0.00) 5 1 767s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 767s 767s Legend: 767s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 767s OPS: Operations Per Second, computed as 1 / Mean 767s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 171 warnings in 281.54s (0:04:41) = 770s Removing patch debian/patches/no_future_dependency.patch 770s Restoring setup.cfg 770s 770s Removing patch debian/patches/32-bit-test.patch 770s Restoring tests/test_io/test_mat.py 770s 770s Removing patch debian/patches/do-not-seek-for-name.patch 770s Restoring src/cobra/io/sbml.py 770s 770s Removing patch debian/patches/ignore_tests.patch 770s Restoring tests/test_io/test_web/test_load.py 770s 770s Removing patch debian/patches/xfail_test_show_versions.patch 770s Restoring tests/test_util/test_util.py 770s 771s Removing patch debian/patches/mathjax.patch 771s Restoring documentation_builder/conf.py 771s 771s No patches applied 771s PASS 771s autopkgtest [21:29:37]: test run-unit-test: -----------------------] 772s run-unit-test PASS 772s autopkgtest [21:29:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 772s autopkgtest [21:29:38]: @@@@@@@@@@@@@@@@@@@@ summary 772s run-unit-test PASS 788s Creating nova instance adt-oracular-arm64-python-cobra-20240503-211646-juju-7f2275-prod-proposed-migration-environment-2-54162f37-3ab9-4c8b-af68-e01c174d37b9 from image adt/ubuntu-oracular-arm64-server-20240503.img (UUID d6f0a588-bf5e-4a78-b5df-9ca1fb1dc89e)...