0s autopkgtest [09:23:37]: starting date and time: 2024-05-05 09:23:37+0000 0s autopkgtest [09:23:37]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [09:23:37]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.af8unbfo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:httpx --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=httpx/0.27.0-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-39.secgroup --name adt-oracular-amd64-python-cobra-20240505-092337-juju-7f2275-prod-proposed-migration-environment-3-b1959de3-ef4d-412a-b79c-76eace324ac4 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 1096s autopkgtest [09:41:53]: testbed dpkg architecture: amd64 1096s autopkgtest [09:41:53]: testbed apt version: 2.7.14build2 1096s autopkgtest [09:41:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1096s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 1096s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 1096s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [110 kB] 1096s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 1096s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1705 kB] 1096s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [195 kB] 1096s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [166 kB] 1096s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [8572 B] 1096s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [1260 B] 1096s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [1346 kB] 1096s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [668 kB] 1096s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [52.6 kB] 1096s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [16.0 kB] 1097s Fetched 4359 kB in 1s (6559 kB/s) 1097s Reading package lists... 1098s Reading package lists... 1099s Building dependency tree... 1099s Reading state information... 1099s Calculating upgrade... 1099s The following packages will be upgraded: 1099s cloud-init ed hdparm hwdata libaio1t64 libdeflate0 libnfnetlink0 1099s libudisks2-0 lsof lto-disabled-list pci.ids udisks2 1099s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1099s Need to get 1866 kB of archives. 1099s After this operation, 75.8 kB of additional disk space will be used. 1099s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 ed amd64 1.20.2-2 [56.3 kB] 1099s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 hdparm amd64 9.65+ds-1.1 [98.3 kB] 1099s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libnfnetlink0 amd64 1.0.2-3 [14.9 kB] 1099s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 lsof amd64 4.95.0-1.1 [247 kB] 1099s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 pci.ids all 0.0~2024.04.20-1 [276 kB] 1099s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 hwdata all 0.380-1 [29.2 kB] 1099s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libaio1t64 amd64 0.3.113-8 [7322 B] 1099s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libdeflate0 amd64 1.20-1 [48.6 kB] 1099s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 udisks2 amd64 2.10.1-7 [297 kB] 1099s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libudisks2-0 amd64 2.10.1-7 [174 kB] 1099s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 lto-disabled-list all 48 [12.3 kB] 1099s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 cloud-init all 24.2~2g51c6569f-0ubuntu1 [606 kB] 1100s Preconfiguring packages ... 1100s Fetched 1866 kB in 0s (8773 kB/s) 1100s (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 ... 73888 files and directories currently installed.) 1100s Preparing to unpack .../00-ed_1.20.2-2_amd64.deb ... 1100s Unpacking ed (1.20.2-2) over (1.20.1-1) ... 1100s Preparing to unpack .../01-hdparm_9.65+ds-1.1_amd64.deb ... 1100s Unpacking hdparm (9.65+ds-1.1) over (9.65+ds-1build1) ... 1100s dpkg: warning: unable to delete old directory '/lib/systemd/system-sleep': Directory not empty 1100s dpkg: warning: unable to delete old directory '/lib/hdparm': Directory not empty 1100s Preparing to unpack .../02-libnfnetlink0_1.0.2-3_amd64.deb ... 1100s Unpacking libnfnetlink0:amd64 (1.0.2-3) over (1.0.2-2build1) ... 1100s Preparing to unpack .../03-lsof_4.95.0-1.1_amd64.deb ... 1100s Unpacking lsof (4.95.0-1.1) over (4.95.0-1build3) ... 1100s Preparing to unpack .../04-pci.ids_0.0~2024.04.20-1_all.deb ... 1100s Unpacking pci.ids (0.0~2024.04.20-1) over (0.0~2024.03.31-1) ... 1100s Preparing to unpack .../05-hwdata_0.380-1_all.deb ... 1100s Unpacking hwdata (0.380-1) over (0.379-1) ... 1100s Preparing to unpack .../06-libaio1t64_0.3.113-8_amd64.deb ... 1100s Unpacking libaio1t64:amd64 (0.3.113-8) over (0.3.113-6build1) ... 1100s Preparing to unpack .../07-libdeflate0_1.20-1_amd64.deb ... 1100s Unpacking libdeflate0:amd64 (1.20-1) over (1.19-1build1) ... 1100s Preparing to unpack .../08-udisks2_2.10.1-7_amd64.deb ... 1100s Unpacking udisks2 (2.10.1-7) over (2.10.1-6build1) ... 1100s Preparing to unpack .../09-libudisks2-0_2.10.1-7_amd64.deb ... 1100s Unpacking libudisks2-0:amd64 (2.10.1-7) over (2.10.1-6build1) ... 1100s Preparing to unpack .../10-lto-disabled-list_48_all.deb ... 1100s Unpacking lto-disabled-list (48) over (47) ... 1100s Preparing to unpack .../11-cloud-init_24.2~2g51c6569f-0ubuntu1_all.deb ... 1101s Unpacking cloud-init (24.2~2g51c6569f-0ubuntu1) over (24.1.3-0ubuntu3) ... 1101s Setting up lto-disabled-list (48) ... 1101s Setting up pci.ids (0.0~2024.04.20-1) ... 1101s Setting up cloud-init (24.2~2g51c6569f-0ubuntu1) ... 1101s Installing new version of config file /etc/cloud/templates/sources.list.ubuntu.deb822.tmpl ... 1102s Setting up libdeflate0:amd64 (1.20-1) ... 1102s Setting up hdparm (9.65+ds-1.1) ... 1102s Installing new version of config file /etc/hdparm.conf ... 1102s Setting up hwdata (0.380-1) ... 1102s Setting up ed (1.20.2-2) ... 1102s Setting up lsof (4.95.0-1.1) ... 1102s Setting up libaio1t64:amd64 (0.3.113-8) ... 1102s Setting up libnfnetlink0:amd64 (1.0.2-3) ... 1102s Setting up libudisks2-0:amd64 (2.10.1-7) ... 1102s Setting up udisks2 (2.10.1-7) ... 1103s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 1103s Processing triggers for man-db (2.12.0-4build2) ... 1104s Processing triggers for dbus (1.14.10-4ubuntu4) ... 1104s Processing triggers for install-info (7.1-3build2) ... 1104s Processing triggers for libc-bin (2.39-0ubuntu8) ... 1105s Reading package lists... 1105s Building dependency tree... 1105s Reading state information... 1105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1105s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 1105s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 1105s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 1105s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 1107s Reading package lists... 1107s Reading package lists... 1107s Building dependency tree... 1107s Reading state information... 1107s Calculating upgrade... 1107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1107s Reading package lists... 1108s Building dependency tree... 1108s Reading state information... 1108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1108s autopkgtest [09:42:05]: rebooting testbed after setup commands that affected boot 1111s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 1124s autopkgtest [09:42:21]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 1125s autopkgtest [09:42:22]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 1126s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 1126s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 1126s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 1127s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 1127s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 1127s gpgv: Can't check signature: No public key 1127s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 1127s autopkgtest [09:42:24]: testing package python-cobra version 0.29.0-1ubuntu2 1127s autopkgtest [09:42:24]: build not needed 1127s autopkgtest [09:42:24]: test run-unit-test: preparing testbed 1128s Reading package lists... 1128s Building dependency tree... 1128s Reading state information... 1128s Starting pkgProblemResolver with broken count: 0 1128s Starting 2 pkgProblemResolver with broken count: 0 1128s Done 1129s The following additional packages will be installed: 1129s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 1129s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 1129s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 1129s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 1129s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 1129s python3-importlib-resources python3-iniconfig python3-more-itertools 1129s python3-mpmath python3-numpy python3-optlang python3-packaging 1129s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 1129s python3-pytest python3-pytest-benchmark python3-pytest-mock 1129s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 1129s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 1129s python3-tabulate python3-zipp quilt swig 1129s Suggested packages: 1129s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 1129s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 1129s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 1129s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 1129s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 1129s swig-doc swig-examples 1129s Recommended packages: 1129s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 1129s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 1129s python3-numba python3-elasticsearch python3-freezegun python3-pygal g++ 1129s | c++-compiler python3-pil isympy-common 1129s The following NEW packages will be installed: 1129s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 1129s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 1129s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 1129s python3-click python3-cobra python3-colorama python3-cpuinfo 1129s python3-dateutil python3-decorator python3-depinfo python3-diskcache 1129s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 1129s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 1129s python3-optlang python3-packaging python3-pandas python3-pandas-lib 1129s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 1129s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 1129s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 1129s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 1129s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 1129s Need to get 51.0 MB/51.0 MB of archives. 1129s After this operation, 239 MB of additional disk space will be used. 1129s Get:1 /tmp/autopkgtest.o2XaqS/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [764 B] 1129s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 diffstat amd64 1.66-1build1 [29.7 kB] 1129s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14-20240412-0ubuntu1 [147 kB] 1129s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext amd64 0.21-14ubuntu2 [864 kB] 1129s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libsuitesparseconfig7 amd64 1:7.6.1+dfsg-1build1 [12.9 kB] 1129s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libamd3 amd64 1:7.6.1+dfsg-1build1 [27.2 kB] 1129s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 1129s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libcolamd3 amd64 1:7.6.1+dfsg-1build1 [19.4 kB] 1129s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14-20240412-0ubuntu1 [924 kB] 1129s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libltdl7 amd64 2.4.7-7build1 [40.3 kB] 1129s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 1129s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 1129s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1129s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12t64 amd64 3.12.3-1 [2339 kB] 1129s Get:15 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 1129s Get:16 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sniffio all 1.3.0-2 [7216 B] 1129s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-anyio all 4.2.0-1 [56.5 kB] 1129s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 1129s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 1129s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.6-2 [79.0 kB] 1129s Get:21 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-depinfo amd64 2.2.0-2 [10.9 kB] 1129s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-diskcache all 5.6.3-1 [35.1 kB] 1129s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h11 all 0.14.0-1 [51.1 kB] 1129s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-httpcore all 1.0.2-2 [38.3 kB] 1129s Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-httpx all 0.27.0-1 [60.9 kB] 1129s Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-more-itertools all 10.2.0-1 [52.9 kB] 1129s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-zipp all 1.0.0-6 [6090 B] 1129s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-importlib-resources all 6.0.1-1 [22.1 kB] 1129s Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-6ubuntu1 [4437 kB] 1129s Get:30 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-swiglpk amd64 5.0.10-1build1 [70.3 kB] 1129s Get:31 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.2.1-3 [421 kB] 1129s Get:32 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-7 [3966 kB] 1129s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-optlang all 1.8.1-1 [82.7 kB] 1129s Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 1129s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-7 [4450 kB] 1129s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-7 [3042 kB] 1129s Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pydantic amd64 1.10.14-1 [1856 kB] 1129s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ruamel.yaml.clib amd64 0.2.8-1build1 [132 kB] 1129s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ruamel.yaml all 0.17.21-1 [86.6 kB] 1129s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-simplejson amd64 3.19.2-1build2 [54.5 kB] 1129s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tabulate all 0.8.10-1 [38.2 kB] 1129s Get:42 http://ftpmaster.internal/ubuntu oracular/universe amd64 swig amd64 4.2.0-2ubuntu1 [1187 kB] 1129s Get:43 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sbml5 amd64 5.20.2+dfsg-3 [3745 kB] 1129s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cobra amd64 0.29.0-1ubuntu2 [1119 kB] 1129s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cpuinfo all 9.0.0-1 [21.2 kB] 1129s Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1129s Get:47 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1129s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 1129s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.4.0-1 [20.4 kB] 1129s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 1129s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 1129s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 1129s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 quilt all 0.67+really0.67-4 [436 kB] 1129s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-6build1 [15.5 MB] 1130s Fetched 51.0 MB in 0s (116 MB/s) 1130s Selecting previously unselected package diffstat. 1130s (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 ... 73894 files and directories currently installed.) 1130s Preparing to unpack .../00-diffstat_1.66-1build1_amd64.deb ... 1130s Unpacking diffstat (1.66-1build1) ... 1130s Selecting previously unselected package libgomp1:amd64. 1130s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_amd64.deb ... 1130s Unpacking libgomp1:amd64 (14-20240412-0ubuntu1) ... 1130s Selecting previously unselected package gettext. 1130s Preparing to unpack .../02-gettext_0.21-14ubuntu2_amd64.deb ... 1130s Unpacking gettext (0.21-14ubuntu2) ... 1130s Selecting previously unselected package libsuitesparseconfig7:amd64. 1130s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_amd64.deb ... 1130s Unpacking libsuitesparseconfig7:amd64 (1:7.6.1+dfsg-1build1) ... 1130s Selecting previously unselected package libamd3:amd64. 1130s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_amd64.deb ... 1130s Unpacking libamd3:amd64 (1:7.6.1+dfsg-1build1) ... 1130s Selecting previously unselected package libblas3:amd64. 1130s Preparing to unpack .../05-libblas3_3.12.0-3build1_amd64.deb ... 1130s Unpacking libblas3:amd64 (3.12.0-3build1) ... 1130s Selecting previously unselected package libcolamd3:amd64. 1130s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_amd64.deb ... 1130s Unpacking libcolamd3:amd64 (1:7.6.1+dfsg-1build1) ... 1130s Selecting previously unselected package libgfortran5:amd64. 1130s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_amd64.deb ... 1130s Unpacking libgfortran5:amd64 (14-20240412-0ubuntu1) ... 1130s Selecting previously unselected package libltdl7:amd64. 1130s Preparing to unpack .../08-libltdl7_2.4.7-7build1_amd64.deb ... 1130s Unpacking libltdl7:amd64 (2.4.7-7build1) ... 1130s Selecting previously unselected package libglpk40:amd64. 1130s Preparing to unpack .../09-libglpk40_5.0-1build2_amd64.deb ... 1130s Unpacking libglpk40:amd64 (5.0-1build2) ... 1130s Selecting previously unselected package liblapack3:amd64. 1130s Preparing to unpack .../10-liblapack3_3.12.0-3build1_amd64.deb ... 1130s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 1131s Selecting previously unselected package liblbfgsb0:amd64. 1131s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 1131s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1131s Selecting previously unselected package libpython3.12t64:amd64. 1131s Preparing to unpack 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.../23-python3-httpx_0.27.0-1_all.deb ... 1131s Unpacking python3-httpx (0.27.0-1) ... 1131s Selecting previously unselected package python3-more-itertools. 1131s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 1131s Unpacking python3-more-itertools (10.2.0-1) ... 1131s Selecting previously unselected package python3-zipp. 1131s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 1131s Unpacking python3-zipp (1.0.0-6) ... 1131s Selecting previously unselected package python3-importlib-resources. 1131s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 1131s Unpacking python3-importlib-resources (6.0.1-1) ... 1131s Selecting previously unselected package python3-numpy. 1131s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_amd64.deb ... 1131s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 1131s Selecting previously unselected package python3-swiglpk. 1131s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_amd64.deb ... 1131s Unpacking python3-swiglpk (5.0.10-1build1) ... 1131s Selecting previously unselected package python3-mpmath. 1131s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 1131s Unpacking python3-mpmath (1.2.1-3) ... 1131s Selecting previously unselected package python3-sympy. 1131s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 1131s Unpacking python3-sympy (1.12-7) ... 1132s Selecting previously unselected package python3-optlang. 1132s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 1132s Unpacking python3-optlang (1.8.1-1) ... 1132s Selecting previously unselected package python3-dateutil. 1132s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 1132s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 1132s Selecting previously unselected package python3-pandas-lib:amd64. 1132s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_amd64.deb ... 1132s Unpacking python3-pandas-lib:amd64 (2.1.4+dfsg-7) ... 1132s Selecting previously unselected package python3-pandas. 1132s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 1132s Unpacking python3-pandas (2.1.4+dfsg-7) ... 1132s Selecting previously unselected package python3-pydantic. 1132s Preparing to unpack .../35-python3-pydantic_1.10.14-1_amd64.deb ... 1132s Unpacking python3-pydantic (1.10.14-1) ... 1132s Selecting previously unselected package python3-ruamel.yaml.clib:amd64. 1132s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8-1build1_amd64.deb ... 1132s Unpacking python3-ruamel.yaml.clib:amd64 (0.2.8-1build1) ... 1132s Selecting previously unselected package python3-ruamel.yaml. 1132s Preparing to unpack .../37-python3-ruamel.yaml_0.17.21-1_all.deb ... 1132s Unpacking python3-ruamel.yaml (0.17.21-1) ... 1132s Selecting previously unselected package python3-simplejson. 1132s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_amd64.deb ... 1132s Unpacking python3-simplejson (3.19.2-1build2) ... 1132s Selecting previously unselected package python3-tabulate. 1132s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 1132s Unpacking python3-tabulate (0.8.10-1) ... 1132s Selecting previously unselected package swig. 1132s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_amd64.deb ... 1132s Unpacking swig (4.2.0-2ubuntu1) ... 1132s Selecting previously unselected package python3-sbml5. 1132s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_amd64.deb ... 1132s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 1133s Selecting previously unselected package python3-cobra. 1133s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_amd64.deb ... 1133s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 1133s Selecting previously unselected package python3-cpuinfo. 1133s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 1133s Unpacking python3-cpuinfo (9.0.0-1) ... 1133s Selecting previously unselected package python3-decorator. 1133s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 1133s Unpacking python3-decorator (5.1.1-5) ... 1133s Selecting previously unselected package python3-iniconfig. 1133s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 1133s Unpacking python3-iniconfig (1.1.1-2) ... 1133s Selecting previously unselected package python3-packaging. 1133s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 1133s Unpacking python3-packaging (24.0-1) ... 1133s Selecting previously unselected package python3-pluggy. 1133s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 1133s Unpacking python3-pluggy (1.4.0-1) ... 1133s Selecting previously unselected package python3-pytest. 1133s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 1133s Unpacking python3-pytest (7.4.4-1) ... 1133s Selecting previously unselected package python3-pytest-benchmark. 1133s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 1133s Unpacking python3-pytest-benchmark (4.0.0-3) ... 1133s Selecting previously unselected package python3-pytest-mock. 1133s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 1133s Unpacking python3-pytest-mock (3.12.0-1.1) ... 1133s Selecting previously unselected package quilt. 1133s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 1133s Unpacking quilt (0.67+really0.67-4) ... 1133s Selecting previously unselected package python3-scipy. 1133s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_amd64.deb ... 1133s Unpacking python3-scipy (1.11.4-6build1) ... 1133s Selecting previously unselected package autopkgtest-satdep. 1133s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 1133s Unpacking autopkgtest-satdep (0) ... 1133s Setting up python3-more-itertools (10.2.0-1) ... 1134s Setting up python3-iniconfig (1.1.1-2) ... 1134s Setting up python3-sniffio (1.3.0-2) ... 1134s Setting up swig (4.2.0-2ubuntu1) ... 1134s Setting up python3-anyio (4.2.0-1) ... 1134s Setting up python3-colorama (0.4.6-4) ... 1134s Setting up python3-ruamel.yaml.clib:amd64 (0.2.8-1build1) ... 1134s Setting up python3-tabulate (0.8.10-1) ... 1134s Setting up python3-zipp (1.0.0-6) ... 1134s Setting up libgomp1:amd64 (14-20240412-0ubuntu1) ... 1134s Setting up python3-click (8.1.6-2) ... 1135s Setting up libpython3.12t64:amd64 (3.12.3-1) ... 1135s Setting up python3-simplejson (3.19.2-1build2) ... 1135s Setting up python3-decorator (5.1.1-5) ... 1135s Setting up libblas3:amd64 (3.12.0-3build1) ... 1135s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 1135s Setting up python3-packaging (24.0-1) ... 1135s Setting up python3-pydantic (1.10.14-1) ... 1135s Setting up diffstat (1.66-1build1) ... 1135s Setting up python3-h11 (0.14.0-1) ... 1135s Setting up python3-depinfo (2.2.0-2) ... 1135s Setting up python3-cpuinfo (9.0.0-1) ... 1136s Setting up libltdl7:amd64 (2.4.7-7build1) ... 1136s Setting up libgfortran5:amd64 (14-20240412-0ubuntu1) ... 1136s Setting up python3-pluggy (1.4.0-1) ... 1136s Setting up python3-ruamel.yaml (0.17.21-1) ... 1136s Setting up libsuitesparseconfig7:amd64 (1:7.6.1+dfsg-1build1) ... 1136s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 1136s Setting up python3-mpmath (1.2.1-3) ... 1137s Setting up python3-diskcache (5.6.3-1) ... 1137s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 1137s Setting up python3-appdirs (1.4.4-4) ... 1137s Setting up python3-httpcore (1.0.2-2) ... 1137s Setting up python3-sympy (1.12-7) ... 1143s Setting up liblapack3:amd64 (3.12.0-3build1) ... 1143s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 1143s Setting up gettext (0.21-14ubuntu2) ... 1143s Setting up libamd3:amd64 (1:7.6.1+dfsg-1build1) ... 1143s Setting up python3-importlib-resources (6.0.1-1) ... 1143s Setting up libcolamd3:amd64 (1:7.6.1+dfsg-1build1) ... 1143s Setting up python3-pytest (7.4.4-1) ... 1143s Setting up quilt (0.67+really0.67-4) ... 1143s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 1144s Setting up python3-httpx (0.27.0-1) ... 1144s Setting up libglpk40:amd64 (5.0-1build2) ... 1144s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 1146s Setting up python3-pytest-mock (3.12.0-1.1) ... 1146s Setting up python3-swiglpk (5.0.10-1build1) ... 1146s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1146s Setting up python3-optlang (1.8.1-1) ... 1146s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 1146s """A representation of the convex optimizatgion problem in standard form. 1146s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 1146s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 1146s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 1146s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 1146s Setting up python3-pytest-benchmark (4.0.0-3) ... 1146s Setting up python3-scipy (1.11.4-6build1) ... 1149s Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-7) ... 1149s Setting up python3-pandas (2.1.4+dfsg-7) ... 1154s Setting up python3-cobra (0.29.0-1ubuntu2) ... 1154s Setting up autopkgtest-satdep (0) ... 1154s Processing triggers for man-db (2.12.0-4build2) ... 1154s Processing triggers for install-info (7.1-3build2) ... 1155s Processing triggers for libc-bin (2.39-0ubuntu8) ... 1157s (Reading database ... 81904 files and directories currently installed.) 1157s Removing autopkgtest-satdep (0) ... 1157s autopkgtest [09:42:54]: test run-unit-test: [----------------------- 1157s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 1157s Running Tests 1157s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 1160s ============================= test session starts ============================== 1160s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 1160s 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) 1160s rootdir: /tmp/autopkgtest.o2XaqS/autopkgtest_tmp 1160s plugins: mock-3.12.0, benchmark-4.0.0, anyio-4.2.0 1160s collected 551 items 1160s 1161s tests/test_core/test_configuration.py ...... [ 1%] 1166s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 1167s ...................x....... [ 12%] 1167s tests/test_core/test_dictlist.py ...................... [ 16%] 1167s tests/test_core/test_formula.py ..... [ 17%] 1167s tests/test_core/test_gene.py . [ 17%] 1167s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 1177s .......................... [ 29%] 1177s tests/test_core/test_group.py .. [ 30%] 1177s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 1186s tests/test_core/test_model.py .......................................... [ 39%] 1187s ...........s..s.ss. [ 43%] 1187s tests/test_core/test_solution.py .ss [ 43%] 1193s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 1194s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 1198s tests/test_flux_analysis/test_geometric.py .. [ 46%] 1198s tests/test_flux_analysis/test_moma.py . [ 46%] 1202s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 1202s tests/test_flux_analysis/test_reaction.py . [ 47%] 1205s tests/test_flux_analysis/test_room.py .... [ 47%] 1210s tests/test_flux_analysis/test_variability.py ....... [ 49%] 1210s tests/test_flux_analysis/test_deletion.py sss [ 49%] 1210s tests/test_flux_analysis/test_moma.py s [ 49%] 1215s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 1218s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 1218s tests/test_flux_analysis/test_helpers.py ... [ 51%] 1219s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 1222s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 1222s tests/test_flux_analysis/test_variability.py ....... [ 54%] 1223s tests/test_io/test_annotation.py .. [ 55%] 1223s tests/test_io/test_annotation_format.py .. [ 55%] 1226s tests/test_io/test_io_order.py ........................... [ 60%] 1226s tests/test_io/test_json.py .... [ 61%] 1243s tests/test_io/test_mat.py ............... [ 64%] 1243s tests/test_io/test_notes.py . [ 64%] 1243s tests/test_io/test_pickle.py .. [ 64%] 1250s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 1250s tests/test_io/test_yaml.py .x [ 72%] 1250s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 1250s tests/test_manipulation/test_annotate.py . [ 73%] 1251s tests/test_manipulation/test_delete.py ....... [ 75%] 1251s tests/test_manipulation/test_modify.py ... [ 75%] 1251s tests/test_manipulation/test_validate.py .. [ 76%] 1251s tests/test_medium/test_boundary_types.py ......... [ 77%] 1253s tests/test_medium/test_minimal_medium.py .......... [ 79%] 1255s tests/test_sampling/test_achr.py ...... [ 80%] 1258s tests/test_sampling/test_optgp.py ...... [ 81%] 1263s tests/test_sampling/test_sampling.py .......... [ 83%] 1265s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 1267s tests/test_summary/test_model_summary.py ............... [ 89%] 1268s tests/test_summary/test_reaction_summary.py .................... [ 92%] 1268s tests/test_util/test_array.py .. [ 93%] 1268s tests/test_util/test_context.py ... [ 93%] 1269s tests/test_util/test_process_pool.py ............... [ 96%] 1270s tests/test_util/test_solver.py ..............s [ 99%] 1270s tests/test_util/test_util.py ...X [100%] 1270s 1270s =============================== warnings summary =============================== 1270s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 1270s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 1270s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 1270s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 1270s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 1270s /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)'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 1270s warn( 1270s 1270s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 1270s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 1270s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 1270s warn( 1270s 1270s tests/test_core/test_model.py::test_reaction_delete 1270s tests/test_core/test_model.py::test_reaction_delete 1270s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 1270s warn( 1270s 1270s tests/test_core/test_model.py::test_group_loss_of_elements 1270s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 1270s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 1270s warn("need to pass in a list") 1270s 1270s tests/test_core/test_model.py::test_change_objective 1270s tests/test_core/test_model.py::test_change_objective 1270s tests/test_core/test_model.py::test_change_objective 1270s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 1270s warn("Please use reaction.flux instead.", DeprecationWarning) 1270s 1270s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 1270s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 1270s /tmp/autopkgtest.o2XaqS/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 1270s assert math.isnan(sol.growth) 1270s 1270s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 1270s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 1270s /tmp/autopkgtest.o2XaqS/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 1270s assert math.isnan(sol_one.growth) 1270s 1270s tests/test_io/test_json.py: 1 warning 1270s tests/test_io/test_mat.py: 5 warnings 1270s tests/test_io/test_pickle.py: 1 warning 1270s tests/test_io/test_sbml.py: 9 warnings 1270s tests/test_io/test_yaml.py: 1 warning 1270s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 1270s warn(f"Solver status is '{status}'.", UserWarning) 1270s 1270s tests/test_medium/test_boundary_types.py: 96 warnings 1270s /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]` 1270s return most[0] 1270s 1270s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 1270s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 1270s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 1270s /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]` 1270s compartment = most[matches[most]][0] 1270s 1270s tests/test_util/test_process_pool.py::test_with_context 1270s /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 1270s self._pool.__enter__() 1270s 1270s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1270s 1270s -------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests --------------------------------------------------------------------------------------------------------------------- 1270s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 1270s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1270s test_subtract_metabolite_benchmark[gurobi] 3.3920 (1.0) 28.4810 (1.0) 3.6740 (1.0) 0.9696 (1.0) 3.5540 (1.0) 0.1100 (1.55) 128;244 272,182.4977 (1.0) 6156 1 1270s test_subtract_metabolite_benchmark[glpk] 3.4460 (1.02) 33.1840 (1.17) 3.7661 (1.03) 1.2037 (1.24) 3.5680 (1.00) 0.0710 (1.0) 167;541 265,528.3577 (0.98) 5191 1 1270s test_subtract_metabolite_benchmark[cplex] 3.4770 (1.03) 89.5260 (3.14) 3.7823 (1.03) 1.6000 (1.65) 3.6680 (1.03) 0.0810 (1.14) 34;237 264,391.0116 (0.97) 4266 1 1270s test_achr_sample_benchmark 170.5560 (50.28) 421.7660 (14.81) 188.2441 (51.24) 21.2219 (21.89) 179.2650 (50.44) 17.4230 (245.39) 177;115 5,312.2524 (0.02) 1847 1 1270s test_change_objective_benchmark[optlang-glpk] 209.4800 (61.76) 1,194.0290 (41.92) 240.1885 (65.38) 40.1000 (41.36) 227.4850 (64.01) 35.8070 (504.32) 567;331 4,163.3965 (0.02) 4795 1 1270s test_optgp_sample_benchmark 256.1330 (75.51) 2,534.6780 (89.00) 285.4968 (77.71) 64.2420 (66.25) 273.2620 (76.89) 24.4415 (344.25) 154;240 3,502.6664 (0.01) 1824 1 1270s test_loopless_benchmark_after 926.9610 (273.28) 3,288.6820 (115.47) 1,057.5225 (287.84) 205.3962 (211.83) 997.3990 (280.64) 116.0420 (>1000.0) 32;36 945.6064 (0.00) 354 1 1270s test_single_gene_deletion_fba_benchmark[glpk] 4,004.0630 (>1000.0) 5,725.9220 (201.04) 4,318.3197 (>1000.0) 247.9750 (255.74) 4,261.1070 (>1000.0) 247.3300 (>1000.0) 30;7 231.5716 (0.00) 178 1 1270s test_minimal_medium_linear_benchmark 5,431.9970 (>1000.0) 6,922.4910 (243.06) 5,745.6009 (>1000.0) 260.8073 (268.97) 5,665.4700 (>1000.0) 254.7060 (>1000.0) 16;5 174.0462 (0.00) 102 1 1270s test_minimal_medium_mip_benchmark 5,435.6180 (>1000.0) 7,370.1680 (258.77) 5,835.2189 (>1000.0) 368.2980 (379.83) 5,685.2540 (>1000.0) 357.7635 (>1000.0) 15;10 171.3732 (0.00) 105 1 1270s test_loopless_benchmark_before 5,654.8290 (>1000.0) 9,220.1040 (323.73) 6,592.1658 (>1000.0) 1,017.4514 (>1000.0) 6,230.1340 (>1000.0) 894.2683 (>1000.0) 11;10 151.6952 (0.00) 79 1 1270s test_copy_benchmark[optlang-glpk] 16,332.0990 (>1000.0) 228,382.7410 (>1000.0) 21,407.6334 (>1000.0) 27,918.1957 (>1000.0) 17,858.0930 (>1000.0) 1,304.4010 (>1000.0) 1;2 46.7123 (0.00) 57 1 1270s test_flux_variability_loopless_benchmark[glpk] 21,603.2520 (>1000.0) 33,702.2410 (>1000.0) 24,257.3799 (>1000.0) 3,660.4962 (>1000.0) 22,893.2780 (>1000.0) 2,439.9937 (>1000.0) 2;2 41.2246 (0.00) 17 1 1270s test_single_reaction_deletion_benchmark[glpk] 24,763.7600 (>1000.0) 27,656.0360 (971.03) 25,641.8254 (>1000.0) 720.0031 (742.55) 25,376.9215 (>1000.0) 1,037.9460 (>1000.0) 9;1 38.9988 (0.00) 38 1 1270s test_gpr_equality_benchmark 26,029.8950 (>1000.0) 32,658.5220 (>1000.0) 28,180.8739 (>1000.0) 1,276.1937 (>1000.0) 27,960.1885 (>1000.0) 1,204.9310 (>1000.0) 8;2 35.4851 (0.00) 34 1 1270s test_deepcopy_benchmark 26,628.8350 (>1000.0) 375,675.8430 (>1000.0) 40,041.4440 (>1000.0) 62,322.5073 (>1000.0) 28,368.4310 (>1000.0) 1,361.1495 (>1000.0) 1;5 24.9741 (0.00) 31 1 1270s test_add_metabolite_benchmark[glpk] 60,290.2060 (>1000.0) 67,288.0030 (>1000.0) 62,536.9573 (>1000.0) 2,488.6254 (>1000.0) 61,477.2600 (>1000.0) 2,499.1633 (>1000.0) 3;2 15.9905 (0.00) 17 1 1270s test_fastcc_benchmark[glpk] 60,916.3920 (>1000.0) 67,237.7860 (>1000.0) 63,022.5053 (>1000.0) 1,768.6605 (>1000.0) 62,837.3280 (>1000.0) 1,883.3320 (>1000.0) 6;1 15.8673 (0.00) 16 1 1270s test_add_metabolite_benchmark[gurobi] 61,389.1540 (>1000.0) 65,872.2460 (>1000.0) 63,535.8628 (>1000.0) 1,455.7418 (>1000.0) 63,498.8020 (>1000.0) 2,653.3990 (>1000.0) 7;0 15.7391 (0.00) 17 1 1270s test_add_metabolite_benchmark[cplex] 61,475.5240 (>1000.0) 114,445.2440 (>1000.0) 72,394.6596 (>1000.0) 13,938.2562 (>1000.0) 67,065.8405 (>1000.0) 6,599.8455 (>1000.0) 2;3 13.8132 (0.00) 16 1 1270s test_double_reaction_deletion_benchmark 62,300.6010 (>1000.0) 70,536.3810 (>1000.0) 65,726.9120 (>1000.0) 3,446.3345 (>1000.0) 65,113.8780 (>1000.0) 5,727.9600 (>1000.0) 1;0 15.2145 (0.00) 5 1 1270s test_optgp_init_benchmark 92,834.5060 (>1000.0) 568,459.5080 (>1000.0) 139,115.0329 (>1000.0) 142,413.1103 (>1000.0) 95,726.4450 (>1000.0) 3,302.5912 (>1000.0) 1;1 7.1883 (0.00) 11 1 1270s test_achr_init_benchmark 93,138.1000 (>1000.0) 100,649.0370 (>1000.0) 95,774.8585 (>1000.0) 2,304.5607 (>1000.0) 95,943.2960 (>1000.0) 2,317.3348 (>1000.0) 4;1 10.4412 (0.00) 11 1 1270s test_single_gene_deletion_linear_moma_benchmark[glpk] 196,034.4160 (>1000.0) 222,190.0280 (>1000.0) 204,884.4864 (>1000.0) 10,039.2198 (>1000.0) 201,964.9100 (>1000.0) 7,834.1380 (>1000.0) 1;1 4.8808 (0.00) 5 1 1270s test_gpr_symbolism_benchmark 207,157.3170 (>1000.0) 237,151.6570 (>1000.0) 215,916.7310 (>1000.0) 12,107.5661 (>1000.0) 211,763.2410 (>1000.0) 10,273.3225 (>1000.0) 1;1 4.6314 (0.00) 5 1 1270s test_double_gene_deletion_benchmark 242,228.0160 (>1000.0) 369,702.6770 (>1000.0) 278,389.4844 (>1000.0) 51,725.4661 (>1000.0) 259,221.1820 (>1000.0) 38,702.9135 (>1000.0) 1;1 3.5921 (0.00) 5 1 1270s test_pfba_benchmark[glpk] 275,803.2660 (>1000.0) 467,051.5770 (>1000.0) 319,239.0230 (>1000.0) 83,017.7966 (>1000.0) 281,749.3600 (>1000.0) 62,439.3052 (>1000.0) 1;1 3.1324 (0.00) 5 1 1270s test_single_gene_deletion_linear_room_benchmark[glpk] 276,816.7080 (>1000.0) 301,705.1440 (>1000.0) 285,504.2934 (>1000.0) 9,927.2929 (>1000.0) 281,973.2600 (>1000.0) 12,574.1792 (>1000.0) 1;0 3.5026 (0.00) 5 1 1270s test_copy_benchmark_large_model[optlang-glpk] 347,064.8320 (>1000.0) 749,117.3350 (>1000.0) 496,922.1884 (>1000.0) 190,232.0168 (>1000.0) 376,897.4150 (>1000.0) 323,329.7843 (>1000.0) 1;0 2.0124 (0.00) 5 1 1270s test_flux_variability_benchmark[glpk] 387,738.1800 (>1000.0) 395,142.8470 (>1000.0) 390,523.4646 (>1000.0) 3,068.5040 (>1000.0) 389,378.3610 (>1000.0) 4,660.9645 (>1000.0) 1;0 2.5607 (0.00) 5 1 1270s test_geometric_fba_benchmark[glpk] 420,678.7120 (>1000.0) 598,120.6500 (>1000.0) 461,094.6164 (>1000.0) 76,828.9778 (>1000.0) 432,109.5430 (>1000.0) 53,514.1438 (>1000.0) 1;1 2.1688 (0.00) 5 1 1270s -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1270s 1270s Legend: 1270s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 1270s OPS: Operations Per Second, computed as 1 / Mean 1270s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 171 warnings in 111.54s (0:01:51) = 1272s Removing patch debian/patches/no_future_dependency.patch 1272s Restoring setup.cfg 1272s 1272s Removing patch debian/patches/32-bit-test.patch 1272s Restoring tests/test_io/test_mat.py 1272s 1272s Removing patch debian/patches/do-not-seek-for-name.patch 1272s Restoring src/cobra/io/sbml.py 1272s 1272s Removing patch debian/patches/ignore_tests.patch 1272s Restoring tests/test_io/test_web/test_load.py 1272s 1272s Removing patch debian/patches/xfail_test_show_versions.patch 1272s Restoring tests/test_util/test_util.py 1272s 1272s Removing patch debian/patches/mathjax.patch 1272s Restoring documentation_builder/conf.py 1272s 1272s No patches applied 1272s PASS 1273s autopkgtest [09:44:50]: test run-unit-test: -----------------------] 1273s run-unit-test PASS 1273s autopkgtest [09:44:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1273s autopkgtest [09:44:50]: @@@@@@@@@@@@@@@@@@@@ summary 1273s run-unit-test PASS 1283s Creating nova instance adt-oracular-amd64-python-cobra-20240505-092337-juju-7f2275-prod-proposed-migration-environment-3-b1959de3-ef4d-412a-b79c-76eace324ac4 from image adt/ubuntu-oracular-amd64-server-20240503.img (UUID e628c166-7cba-46cd-8ffe-b739924ba328)...