0s autopkgtest [06:40:27]: starting date and time: 2024-05-05 06:40:27+0000 0s autopkgtest [06:40:27]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [06:40:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r6ttyd_f/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml,src:monty,src:ruamel.yaml.clib --apt-upgrade python-cobra --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 monty/2024.4.17-1 ruamel.yaml.clib/0.2.8+ds-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-arm64-22.secgroup --name adt-oracular-arm64-python-cobra-20240505-064027-juju-7f2275-prod-proposed-migration-environment-2-1fddf9e0-a22b-42df-9ee1-ce4f21ae9ae8 --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/ 216s autopkgtest [06:44:03]: testbed dpkg architecture: arm64 217s autopkgtest [06:44:04]: testbed apt version: 2.7.14build2 217s autopkgtest [06:44:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 218s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 218s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 218s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [110 kB] 218s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 218s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1708 kB] 219s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [188 kB] 219s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [13.1 kB] 219s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [1288 kB] 219s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [22.1 kB] 219s Fetched 3420 kB in 2s (2271 kB/s) 219s Reading package lists... 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s Calculating upgrade... 225s The following packages will be upgraded: 225s cloud-init ed hdparm hwdata libaio1t64 libdeflate0 libnfnetlink0 225s libudisks2-0 lsof lto-disabled-list pci.ids udisks2 226s 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 1849 kB of archives. 226s After this operation, 133 kB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 ed arm64 1.20.2-2 [55.9 kB] 226s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 hdparm arm64 9.65+ds-1.1 [95.4 kB] 226s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libnfnetlink0 arm64 1.0.2-3 [14.9 kB] 226s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 lsof arm64 4.95.0-1.1 [245 kB] 226s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 pci.ids all 0.0~2024.04.20-1 [276 kB] 226s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 hwdata all 0.380-1 [29.2 kB] 226s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libaio1t64 arm64 0.3.113-8 [7310 B] 226s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libdeflate0 arm64 1.20-1 [45.3 kB] 226s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 udisks2 arm64 2.10.1-7 [291 kB] 226s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libudisks2-0 arm64 2.10.1-7 [172 kB] 226s Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 lto-disabled-list all 48 [12.3 kB] 226s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 cloud-init all 24.2~2g51c6569f-0ubuntu1 [606 kB] 227s Preconfiguring packages ... 227s Fetched 1849 kB in 1s (2397 kB/s) 227s (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.) 227s Preparing to unpack .../00-ed_1.20.2-2_arm64.deb ... 227s Unpacking ed (1.20.2-2) over (1.20.1-1) ... 227s Preparing to unpack .../01-hdparm_9.65+ds-1.1_arm64.deb ... 227s Unpacking hdparm (9.65+ds-1.1) over (9.65+ds-1build1) ... 227s dpkg: warning: unable to delete old directory '/lib/systemd/system-sleep': Directory not empty 227s dpkg: warning: unable to delete old directory '/lib/hdparm': Directory not empty 227s Preparing to unpack .../02-libnfnetlink0_1.0.2-3_arm64.deb ... 227s Unpacking libnfnetlink0:arm64 (1.0.2-3) over (1.0.2-2build1) ... 227s Preparing to unpack .../03-lsof_4.95.0-1.1_arm64.deb ... 227s Unpacking lsof (4.95.0-1.1) over (4.95.0-1build3) ... 228s Preparing to unpack .../04-pci.ids_0.0~2024.04.20-1_all.deb ... 228s Unpacking pci.ids (0.0~2024.04.20-1) over (0.0~2024.03.31-1) ... 228s Preparing to unpack .../05-hwdata_0.380-1_all.deb ... 228s Unpacking hwdata (0.380-1) over (0.379-1) ... 228s Preparing to unpack .../06-libaio1t64_0.3.113-8_arm64.deb ... 228s Unpacking libaio1t64:arm64 (0.3.113-8) over (0.3.113-6build1) ... 228s Preparing to unpack .../07-libdeflate0_1.20-1_arm64.deb ... 228s Unpacking libdeflate0:arm64 (1.20-1) over (1.19-1build1) ... 228s Preparing to unpack .../08-udisks2_2.10.1-7_arm64.deb ... 228s Unpacking udisks2 (2.10.1-7) over (2.10.1-6build1) ... 228s Preparing to unpack .../09-libudisks2-0_2.10.1-7_arm64.deb ... 228s Unpacking libudisks2-0:arm64 (2.10.1-7) over (2.10.1-6build1) ... 228s Preparing to unpack .../10-lto-disabled-list_48_all.deb ... 228s Unpacking lto-disabled-list (48) over (47) ... 228s Preparing to unpack .../11-cloud-init_24.2~2g51c6569f-0ubuntu1_all.deb ... 228s Unpacking cloud-init (24.2~2g51c6569f-0ubuntu1) over (24.1.3-0ubuntu3) ... 229s Setting up lto-disabled-list (48) ... 229s Setting up pci.ids (0.0~2024.04.20-1) ... 229s Setting up cloud-init (24.2~2g51c6569f-0ubuntu1) ... 229s Installing new version of config file /etc/cloud/templates/sources.list.ubuntu.deb822.tmpl ... 232s Setting up libdeflate0:arm64 (1.20-1) ... 232s Setting up hdparm (9.65+ds-1.1) ... 232s Installing new version of config file /etc/hdparm.conf ... 232s Setting up hwdata (0.380-1) ... 232s Setting up ed (1.20.2-2) ... 232s Setting up lsof (4.95.0-1.1) ... 232s Setting up libaio1t64:arm64 (0.3.113-8) ... 232s Setting up libnfnetlink0:arm64 (1.0.2-3) ... 232s Setting up libudisks2-0:arm64 (2.10.1-7) ... 232s Setting up udisks2 (2.10.1-7) ... 234s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 234s Processing triggers for man-db (2.12.0-4build2) ... 235s Processing triggers for dbus (1.14.10-4ubuntu4) ... 235s Processing triggers for install-info (7.1-3build2) ... 235s Processing triggers for libc-bin (2.39-0ubuntu8) ... 236s Reading package lists... 236s Building dependency tree... 236s Reading state information... 237s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 238s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 238s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 238s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 238s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 241s Reading package lists... 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 242s Calculating upgrade... 243s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 243s Reading package lists... 244s Building dependency tree... 244s Reading state information... 245s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 245s autopkgtest [06:44:32]: rebooting testbed after setup commands that affected boot 250s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 273s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 281s autopkgtest [06:45:08]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 284s autopkgtest [06:45:11]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cobra 287s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (dsc) [3205 B] 287s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (tar) [3650 kB] 287s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cobra 0.29.0-1ubuntu2 (diff) [10.4 kB] 288s gpgv: Signature made Mon Apr 1 07:28:03 2024 UTC 288s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 288s gpgv: Can't check signature: No public key 288s dpkg-source: warning: cannot verify inline signature for ./python-cobra_0.29.0-1ubuntu2.dsc: no acceptable signature found 288s autopkgtest [06:45:15]: testing package python-cobra version 0.29.0-1ubuntu2 289s autopkgtest [06:45:16]: build not needed 289s autopkgtest [06:45:16]: test run-unit-test: preparing testbed 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 292s Starting pkgProblemResolver with broken count: 0 292s Starting 2 pkgProblemResolver with broken count: 0 292s Done 293s The following additional packages will be installed: 293s diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 libglpk40 libgomp1 293s liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 libsuitesparseconfig7 293s python-cobra-data python3-anyio python3-appdirs python3-click python3-cobra 293s python3-colorama python3-cpuinfo python3-dateutil python3-decorator 293s python3-depinfo python3-diskcache python3-h11 python3-httpcore python3-httpx 293s python3-importlib-resources python3-iniconfig python3-more-itertools 293s python3-mpmath python3-numpy python3-optlang python3-packaging 293s python3-pandas python3-pandas-lib python3-pluggy python3-pydantic 293s python3-pytest python3-pytest-benchmark python3-pytest-mock 293s python3-ruamel.yaml python3-ruamel.yaml.clib python3-sbml5 python3-scipy 293s python3-simplejson python3-sniffio python3-swiglpk python3-sympy 293s python3-tabulate python3-zipp quilt swig 293s Suggested packages: 293s autopoint gettext-doc libasprintf-dev libgettextpo-dev libiodbc2-dev 293s default-libmysqlclient-dev python3-matplotlib qsopt-ex python-mpmath-doc 293s python3-gmpy2 gcc gfortran python3-dev python-pandas-doc python3-statsmodels 293s python-pytest-mock-doc python-scipy-doc texlive-fonts-extra dvipng 293s python-sympy-doc default-mta | mail-transport-agent graphviz procmail 293s swig-doc swig-examples 293s Recommended packages: 293s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 293s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 293s python3-elasticsearch python3-freezegun python3-pygal g++ | c++-compiler 293s python3-pil isympy-common 293s The following NEW packages will be installed: 293s autopkgtest-satdep diffstat gettext libamd3 libblas3 libcolamd3 libgfortran5 293s libglpk40 libgomp1 liblapack3 liblbfgsb0 libltdl7 libpython3.12t64 293s libsuitesparseconfig7 python-cobra-data python3-anyio python3-appdirs 293s python3-click python3-cobra python3-colorama python3-cpuinfo 293s python3-dateutil python3-decorator python3-depinfo python3-diskcache 293s python3-h11 python3-httpcore python3-httpx python3-importlib-resources 293s python3-iniconfig python3-more-itertools python3-mpmath python3-numpy 293s python3-optlang python3-packaging python3-pandas python3-pandas-lib 293s python3-pluggy python3-pydantic python3-pytest python3-pytest-benchmark 293s python3-pytest-mock python3-ruamel.yaml python3-ruamel.yaml.clib 293s python3-sbml5 python3-scipy python3-simplejson python3-sniffio 293s python3-swiglpk python3-sympy python3-tabulate python3-zipp quilt swig 294s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 294s Need to get 47.8 MB/47.8 MB of archives. 294s After this operation, 230 MB of additional disk space will be used. 294s Get:1 /tmp/autopkgtest.yZCirX/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [764 B] 294s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 diffstat arm64 1.66-1build1 [28.1 kB] 294s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] 294s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 gettext arm64 0.21-14ubuntu2 [845 kB] 294s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 libsuitesparseconfig7 arm64 1:7.6.1+dfsg-1build1 [12.5 kB] 294s Get:6 http://ftpmaster.internal/ubuntu oracular/universe arm64 libamd3 arm64 1:7.6.1+dfsg-1build1 [25.7 kB] 294s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 294s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libcolamd3 arm64 1:7.6.1+dfsg-1build1 [18.1 kB] 294s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14-20240412-0ubuntu1 [444 kB] 294s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 libltdl7 arm64 2.4.7-7build1 [40.4 kB] 294s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 294s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 295s Get:13 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 295s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libpython3.12t64 arm64 3.12.3-1 [2278 kB] 295s Get:15 http://ftpmaster.internal/ubuntu oracular/universe arm64 python-cobra-data all 0.29.0-1ubuntu2 [1648 kB] 295s Get:16 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sniffio all 1.3.0-2 [7216 B] 295s Get:17 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-anyio all 4.2.0-1 [56.5 kB] 295s Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 295s Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 295s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-click all 8.1.6-2 [79.0 kB] 295s Get:21 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-depinfo arm64 2.2.0-2 [10.9 kB] 295s Get:22 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-diskcache all 5.6.3-1 [35.1 kB] 295s Get:23 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h11 all 0.14.0-1 [51.1 kB] 295s Get:24 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-httpcore all 1.0.2-2 [38.3 kB] 295s Get:25 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-httpx all 0.26.0-2 [61.3 kB] 295s Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 295s Get:27 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-zipp all 1.0.0-6 [6090 B] 295s Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-importlib-resources all 6.0.1-1 [22.1 kB] 295s Get:29 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-6ubuntu1 [3565 kB] 296s Get:30 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-swiglpk arm64 5.0.10-1build1 [71.9 kB] 296s Get:31 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 296s Get:32 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sympy all 1.12-7 [3966 kB] 296s Get:33 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-optlang all 1.8.1-1 [82.7 kB] 296s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dateutil all 2.8.2-3ubuntu1 [79.4 kB] 296s Get:35 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-7 [4178 kB] 296s Get:36 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas all 2.1.4+dfsg-7 [3042 kB] 296s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pydantic arm64 1.10.14-1 [1688 kB] 296s Get:38 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-1 [127 kB] 296s Get:39 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 296s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-simplejson arm64 3.19.2-1build2 [53.6 kB] 296s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB] 296s Get:42 http://ftpmaster.internal/ubuntu oracular/universe arm64 swig arm64 4.2.0-2ubuntu1 [1152 kB] 296s Get:43 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sbml5 arm64 5.20.2+dfsg-3 [3539 kB] 297s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cobra arm64 0.29.0-1ubuntu2 [1119 kB] 297s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cpuinfo all 9.0.0-1 [21.2 kB] 297s Get:46 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 297s Get:47 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 297s Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 297s Get:49 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 297s Get:50 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 297s Get:51 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest-benchmark all 4.0.0-3 [38.2 kB] 297s Get:52 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pytest-mock all 3.12.0-1.1 [11.3 kB] 297s Get:53 http://ftpmaster.internal/ubuntu oracular/universe arm64 quilt all 0.67+really0.67-4 [436 kB] 297s Get:54 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.11.4-6build1 [15.0 MB] 298s Fetched 47.8 MB in 4s (13.4 MB/s) 298s Selecting previously unselected package diffstat. 298s (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 ... 77900 files and directories currently installed.) 298s Preparing to unpack .../00-diffstat_1.66-1build1_arm64.deb ... 298s Unpacking diffstat (1.66-1build1) ... 298s Selecting previously unselected package libgomp1:arm64. 298s Preparing to unpack .../01-libgomp1_14-20240412-0ubuntu1_arm64.deb ... 298s Unpacking libgomp1:arm64 (14-20240412-0ubuntu1) ... 298s Selecting previously unselected package gettext. 298s Preparing to unpack .../02-gettext_0.21-14ubuntu2_arm64.deb ... 298s Unpacking gettext (0.21-14ubuntu2) ... 298s Selecting previously unselected package libsuitesparseconfig7:arm64. 298s Preparing to unpack .../03-libsuitesparseconfig7_1%3a7.6.1+dfsg-1build1_arm64.deb ... 298s Unpacking libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 298s Selecting previously unselected package libamd3:arm64. 298s Preparing to unpack .../04-libamd3_1%3a7.6.1+dfsg-1build1_arm64.deb ... 298s Unpacking libamd3:arm64 (1:7.6.1+dfsg-1build1) ... 298s Selecting previously unselected package libblas3:arm64. 299s Preparing to unpack .../05-libblas3_3.12.0-3build1_arm64.deb ... 299s Unpacking libblas3:arm64 (3.12.0-3build1) ... 299s Selecting previously unselected package libcolamd3:arm64. 299s Preparing to unpack .../06-libcolamd3_1%3a7.6.1+dfsg-1build1_arm64.deb ... 299s Unpacking libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 299s Selecting previously unselected package libgfortran5:arm64. 299s Preparing to unpack .../07-libgfortran5_14-20240412-0ubuntu1_arm64.deb ... 299s Unpacking libgfortran5:arm64 (14-20240412-0ubuntu1) ... 299s Selecting previously unselected package libltdl7:arm64. 299s Preparing to unpack .../08-libltdl7_2.4.7-7build1_arm64.deb ... 299s Unpacking libltdl7:arm64 (2.4.7-7build1) ... 299s Selecting previously unselected package libglpk40:arm64. 299s Preparing to unpack .../09-libglpk40_5.0-1build2_arm64.deb ... 299s Unpacking libglpk40:arm64 (5.0-1build2) ... 299s Selecting previously unselected package liblapack3:arm64. 299s Preparing to unpack .../10-liblapack3_3.12.0-3build1_arm64.deb ... 299s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 299s Selecting previously unselected package liblbfgsb0:arm64. 299s Preparing to unpack .../11-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 299s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 299s Selecting previously unselected package libpython3.12t64:arm64. 299s Preparing to unpack .../12-libpython3.12t64_3.12.3-1_arm64.deb ... 299s Unpacking libpython3.12t64:arm64 (3.12.3-1) ... 299s Selecting previously unselected package python-cobra-data. 299s Preparing to unpack .../13-python-cobra-data_0.29.0-1ubuntu2_all.deb ... 299s Unpacking python-cobra-data (0.29.0-1ubuntu2) ... 299s Selecting previously unselected package python3-sniffio. 299s Preparing to unpack .../14-python3-sniffio_1.3.0-2_all.deb ... 299s Unpacking python3-sniffio (1.3.0-2) ... 299s Selecting previously unselected package python3-anyio. 299s Preparing to unpack .../15-python3-anyio_4.2.0-1_all.deb ... 299s Unpacking python3-anyio (4.2.0-1) ... 299s Selecting previously unselected package python3-appdirs. 299s Preparing to unpack .../16-python3-appdirs_1.4.4-4_all.deb ... 299s Unpacking python3-appdirs (1.4.4-4) ... 299s Selecting previously unselected package python3-colorama. 299s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ... 299s Unpacking python3-colorama (0.4.6-4) ... 299s Selecting previously unselected package python3-click. 299s Preparing to unpack .../18-python3-click_8.1.6-2_all.deb ... 300s Unpacking python3-click (8.1.6-2) ... 300s Selecting previously unselected package python3-depinfo. 300s Preparing to unpack .../19-python3-depinfo_2.2.0-2_arm64.deb ... 300s Unpacking python3-depinfo (2.2.0-2) ... 300s Selecting previously unselected package python3-diskcache. 300s Preparing to unpack .../20-python3-diskcache_5.6.3-1_all.deb ... 300s Unpacking python3-diskcache (5.6.3-1) ... 300s Selecting previously unselected package python3-h11. 300s Preparing to unpack .../21-python3-h11_0.14.0-1_all.deb ... 300s Unpacking python3-h11 (0.14.0-1) ... 300s Selecting previously unselected package python3-httpcore. 300s Preparing to unpack .../22-python3-httpcore_1.0.2-2_all.deb ... 300s Unpacking python3-httpcore (1.0.2-2) ... 300s Selecting previously unselected package python3-httpx. 300s Preparing to unpack .../23-python3-httpx_0.26.0-2_all.deb ... 300s Unpacking python3-httpx (0.26.0-2) ... 300s Selecting previously unselected package python3-more-itertools. 300s Preparing to unpack .../24-python3-more-itertools_10.2.0-1_all.deb ... 300s Unpacking python3-more-itertools (10.2.0-1) ... 300s Selecting previously unselected package python3-zipp. 300s Preparing to unpack .../25-python3-zipp_1.0.0-6_all.deb ... 300s Unpacking python3-zipp (1.0.0-6) ... 300s Selecting previously unselected package python3-importlib-resources. 300s Preparing to unpack .../26-python3-importlib-resources_6.0.1-1_all.deb ... 300s Unpacking python3-importlib-resources (6.0.1-1) ... 300s Selecting previously unselected package python3-numpy. 300s Preparing to unpack .../27-python3-numpy_1%3a1.26.4+ds-6ubuntu1_arm64.deb ... 300s Unpacking python3-numpy (1:1.26.4+ds-6ubuntu1) ... 300s Selecting previously unselected package python3-swiglpk. 301s Preparing to unpack .../28-python3-swiglpk_5.0.10-1build1_arm64.deb ... 301s Unpacking python3-swiglpk (5.0.10-1build1) ... 301s Selecting previously unselected package python3-mpmath. 301s Preparing to unpack .../29-python3-mpmath_1.2.1-3_all.deb ... 301s Unpacking python3-mpmath (1.2.1-3) ... 301s Selecting previously unselected package python3-sympy. 301s Preparing to unpack .../30-python3-sympy_1.12-7_all.deb ... 301s Unpacking python3-sympy (1.12-7) ... 301s Selecting previously unselected package python3-optlang. 301s Preparing to unpack .../31-python3-optlang_1.8.1-1_all.deb ... 301s Unpacking python3-optlang (1.8.1-1) ... 301s Selecting previously unselected package python3-dateutil. 301s Preparing to unpack .../32-python3-dateutil_2.8.2-3ubuntu1_all.deb ... 301s Unpacking python3-dateutil (2.8.2-3ubuntu1) ... 301s Selecting previously unselected package python3-pandas-lib:arm64. 301s Preparing to unpack .../33-python3-pandas-lib_2.1.4+dfsg-7_arm64.deb ... 301s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-7) ... 302s Selecting previously unselected package python3-pandas. 302s Preparing to unpack .../34-python3-pandas_2.1.4+dfsg-7_all.deb ... 302s Unpacking python3-pandas (2.1.4+dfsg-7) ... 302s Selecting previously unselected package python3-pydantic. 302s Preparing to unpack .../35-python3-pydantic_1.10.14-1_arm64.deb ... 302s Unpacking python3-pydantic (1.10.14-1) ... 303s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 303s Preparing to unpack .../36-python3-ruamel.yaml.clib_0.2.8+ds-1_arm64.deb ... 303s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 303s Selecting previously unselected package python3-ruamel.yaml. 303s Preparing to unpack .../37-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 303s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 303s Selecting previously unselected package python3-simplejson. 303s Preparing to unpack .../38-python3-simplejson_3.19.2-1build2_arm64.deb ... 303s Unpacking python3-simplejson (3.19.2-1build2) ... 303s Selecting previously unselected package python3-tabulate. 303s Preparing to unpack .../39-python3-tabulate_0.8.10-1_all.deb ... 303s Unpacking python3-tabulate (0.8.10-1) ... 303s Selecting previously unselected package swig. 303s Preparing to unpack .../40-swig_4.2.0-2ubuntu1_arm64.deb ... 303s Unpacking swig (4.2.0-2ubuntu1) ... 303s Selecting previously unselected package python3-sbml5. 303s Preparing to unpack .../41-python3-sbml5_5.20.2+dfsg-3_arm64.deb ... 303s Unpacking python3-sbml5 (5.20.2+dfsg-3) ... 304s Selecting previously unselected package python3-cobra. 304s Preparing to unpack .../42-python3-cobra_0.29.0-1ubuntu2_arm64.deb ... 304s Unpacking python3-cobra (0.29.0-1ubuntu2) ... 304s Selecting previously unselected package python3-cpuinfo. 304s Preparing to unpack .../43-python3-cpuinfo_9.0.0-1_all.deb ... 304s Unpacking python3-cpuinfo (9.0.0-1) ... 304s Selecting previously unselected package python3-decorator. 304s Preparing to unpack .../44-python3-decorator_5.1.1-5_all.deb ... 304s Unpacking python3-decorator (5.1.1-5) ... 304s Selecting previously unselected package python3-iniconfig. 304s Preparing to unpack .../45-python3-iniconfig_1.1.1-2_all.deb ... 304s Unpacking python3-iniconfig (1.1.1-2) ... 304s Selecting previously unselected package python3-packaging. 304s Preparing to unpack .../46-python3-packaging_24.0-1_all.deb ... 304s Unpacking python3-packaging (24.0-1) ... 304s Selecting previously unselected package python3-pluggy. 304s Preparing to unpack .../47-python3-pluggy_1.4.0-1_all.deb ... 304s Unpacking python3-pluggy (1.4.0-1) ... 304s Selecting previously unselected package python3-pytest. 304s Preparing to unpack .../48-python3-pytest_7.4.4-1_all.deb ... 304s Unpacking python3-pytest (7.4.4-1) ... 304s Selecting previously unselected package python3-pytest-benchmark. 304s Preparing to unpack .../49-python3-pytest-benchmark_4.0.0-3_all.deb ... 304s Unpacking python3-pytest-benchmark (4.0.0-3) ... 304s Selecting previously unselected package python3-pytest-mock. 304s Preparing to unpack .../50-python3-pytest-mock_3.12.0-1.1_all.deb ... 304s Unpacking python3-pytest-mock (3.12.0-1.1) ... 304s Selecting previously unselected package quilt. 304s Preparing to unpack .../51-quilt_0.67+really0.67-4_all.deb ... 304s Unpacking quilt (0.67+really0.67-4) ... 304s Selecting previously unselected package python3-scipy. 304s Preparing to unpack .../52-python3-scipy_1.11.4-6build1_arm64.deb ... 304s Unpacking python3-scipy (1.11.4-6build1) ... 305s Selecting previously unselected package autopkgtest-satdep. 305s Preparing to unpack .../53-1-autopkgtest-satdep.deb ... 305s Unpacking autopkgtest-satdep (0) ... 306s Setting up python3-more-itertools (10.2.0-1) ... 306s Setting up python3-iniconfig (1.1.1-2) ... 306s Setting up python3-sniffio (1.3.0-2) ... 307s Setting up swig (4.2.0-2ubuntu1) ... 307s Setting up python3-anyio (4.2.0-1) ... 307s Setting up python3-colorama (0.4.6-4) ... 308s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 308s Setting up python3-tabulate (0.8.10-1) ... 308s Setting up python3-zipp (1.0.0-6) ... 308s Setting up libgomp1:arm64 (14-20240412-0ubuntu1) ... 308s Setting up python3-click (8.1.6-2) ... 309s Setting up libpython3.12t64:arm64 (3.12.3-1) ... 309s Setting up python3-simplejson (3.19.2-1build2) ... 309s Setting up python3-decorator (5.1.1-5) ... 310s Setting up libblas3:arm64 (3.12.0-3build1) ... 310s 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 310s Setting up python3-packaging (24.0-1) ... 310s Setting up python3-pydantic (1.10.14-1) ... 311s Setting up diffstat (1.66-1build1) ... 311s Setting up python3-h11 (0.14.0-1) ... 311s Setting up python3-depinfo (2.2.0-2) ... 312s Setting up python3-cpuinfo (9.0.0-1) ... 312s Setting up libltdl7:arm64 (2.4.7-7build1) ... 312s Setting up libgfortran5:arm64 (14-20240412-0ubuntu1) ... 312s Setting up python3-pluggy (1.4.0-1) ... 312s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 313s Setting up libsuitesparseconfig7:arm64 (1:7.6.1+dfsg-1build1) ... 313s Setting up python3-dateutil (2.8.2-3ubuntu1) ... 313s Setting up python3-mpmath (1.2.1-3) ... 315s Setting up python3-diskcache (5.6.3-1) ... 315s Setting up python-cobra-data (0.29.0-1ubuntu2) ... 315s Setting up python3-appdirs (1.4.4-4) ... 316s Setting up python3-httpcore (1.0.2-2) ... 316s Setting up python3-sympy (1.12-7) ... 330s Setting up liblapack3:arm64 (3.12.0-3build1) ... 330s 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 330s Setting up gettext (0.21-14ubuntu2) ... 330s Setting up libamd3:arm64 (1:7.6.1+dfsg-1build1) ... 330s Setting up python3-importlib-resources (6.0.1-1) ... 330s Setting up libcolamd3:arm64 (1:7.6.1+dfsg-1build1) ... 330s Setting up python3-pytest (7.4.4-1) ... 331s Setting up quilt (0.67+really0.67-4) ... 331s Setting up python3-sbml5 (5.20.2+dfsg-3) ... 332s Setting up python3-httpx (0.26.0-2) ... 332s Setting up libglpk40:arm64 (5.0-1build2) ... 332s Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... 337s Setting up python3-pytest-mock (3.12.0-1.1) ... 337s Setting up python3-swiglpk (5.0.10-1build1) ... 337s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 337s Setting up python3-optlang (1.8.1-1) ... 338s /usr/lib/python3/dist-packages/optlang/matrix_interface.py:60: SyntaxWarning: invalid escape sequence '\m' 338s """A representation of the convex optimizatgion problem in standard form. 338s /usr/lib/python3/dist-packages/optlang/tests/data/parse_the_final_netlib_results.py:36: SyntaxWarning: invalid escape sequence '\*' 338s OBJ_REGEX = re.compile('\* Objvalue : -?\d+/\d+') 338s /usr/lib/python3/dist-packages/optlang/tests/test_cplex_interface.py:222: SyntaxWarning: invalid escape sequence '\s' 338s self.assertRegexpMatches(str(self.model), '\s*Dummy_\d+:\s*y \+ z \+ 2\.333 x - .* = -300') 338s Setting up python3-pytest-benchmark (4.0.0-3) ... 338s Setting up python3-scipy (1.11.4-6build1) ... 345s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-7) ... 345s Setting up python3-pandas (2.1.4+dfsg-7) ... 356s Setting up python3-cobra (0.29.0-1ubuntu2) ... 356s Setting up autopkgtest-satdep (0) ... 356s Processing triggers for man-db (2.12.0-4build2) ... 357s Processing triggers for install-info (7.1-3build2) ... 357s Processing triggers for libc-bin (2.39-0ubuntu8) ... 364s (Reading database ... 85929 files and directories currently installed.) 364s Removing autopkgtest-satdep (0) ... 365s autopkgtest [06:46:32]: test run-unit-test: [----------------------- 365s File series fully applied, ends at patch debian/patches/no_future_dependency.patch 365s Running Tests 365s Since python3-sbml5 can only deal with one Python3 version we restrict the test to default Python3 373s ============================= test session starts ============================== 373s platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.4.0 373s 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) 373s rootdir: /tmp/autopkgtest.yZCirX/autopkgtest_tmp 373s plugins: mock-3.12.0, benchmark-4.0.0, anyio-4.2.0 373s collected 551 items 373s 373s tests/test_core/test_configuration.py ...... [ 1%] 381s tests/test_core/test_core_reaction.py ..........ss...................... [ 7%] 383s ...................x....... [ 12%] 383s tests/test_core/test_dictlist.py ...................... [ 16%] 383s tests/test_core/test_formula.py ..... [ 17%] 383s tests/test_core/test_gene.py . [ 17%] 384s tests/test_core/test_gpr.py .....................x..x................... [ 25%] 407s .......................... [ 29%] 407s tests/test_core/test_group.py .. [ 30%] 407s tests/test_core/test_metabolite.py ...ss.ss. [ 31%] 427s tests/test_core/test_model.py .......................................... [ 39%] 430s ...........s..s.ss. [ 43%] 430s tests/test_core/test_solution.py .ss [ 43%] 443s tests/test_flux_analysis/test_deletion.py ....s..... [ 45%] 444s tests/test_flux_analysis/test_fastcc.py .... [ 46%] 453s tests/test_flux_analysis/test_geometric.py .. [ 46%] 454s tests/test_flux_analysis/test_moma.py . [ 46%] 464s tests/test_flux_analysis/test_parsimonious.py .. [ 47%] 464s tests/test_flux_analysis/test_reaction.py . [ 47%] 472s tests/test_flux_analysis/test_room.py .... [ 47%] 485s tests/test_flux_analysis/test_variability.py ....... [ 49%] 485s tests/test_flux_analysis/test_deletion.py sss [ 49%] 485s tests/test_flux_analysis/test_moma.py s [ 49%] 499s tests/test_flux_analysis/test_deletion.py ...... [ 50%] 506s tests/test_flux_analysis/test_gapfilling.py . [ 51%] 506s tests/test_flux_analysis/test_helpers.py ... [ 51%] 508s tests/test_flux_analysis/test_loopless.py ..... [ 52%] 514s tests/test_flux_analysis/test_phenotype_phase_plane.py ...... [ 53%] 516s tests/test_flux_analysis/test_variability.py ....... [ 54%] 516s tests/test_io/test_annotation.py .. [ 55%] 516s tests/test_io/test_annotation_format.py .. [ 55%] 525s tests/test_io/test_io_order.py ........................... [ 60%] 525s tests/test_io/test_json.py .... [ 61%] 575s tests/test_io/test_mat.py ............... [ 64%] 575s tests/test_io/test_notes.py . [ 64%] 575s tests/test_io/test_pickle.py .. [ 64%] 593s tests/test_io/test_sbml.py .ssss............xxxx.x.x..s............. [ 72%] 593s tests/test_io/test_yaml.py .x [ 72%] 594s tests/test_io/test_web/test_load.py ..ssss. [ 73%] 594s tests/test_manipulation/test_annotate.py . [ 73%] 597s tests/test_manipulation/test_delete.py ....... [ 75%] 597s tests/test_manipulation/test_modify.py ... [ 75%] 597s tests/test_manipulation/test_validate.py .. [ 76%] 598s tests/test_medium/test_boundary_types.py ......... [ 77%] 600s tests/test_medium/test_minimal_medium.py .......... [ 79%] 604s tests/test_sampling/test_achr.py ...... [ 80%] 608s tests/test_sampling/test_optgp.py ...... [ 81%] 628s tests/test_sampling/test_sampling.py .......... [ 83%] 632s tests/test_summary/test_metabolite_summary.py ................. [ 86%] 635s tests/test_summary/test_model_summary.py ............... [ 89%] 639s tests/test_summary/test_reaction_summary.py .................... [ 92%] 639s tests/test_util/test_array.py .. [ 93%] 639s tests/test_util/test_context.py ... [ 93%] 642s tests/test_util/test_process_pool.py ............... [ 96%] 645s tests/test_util/test_solver.py ..............s [ 99%] 645s tests/test_util/test_util.py ...X [100%] 645s 645s =============================== warnings summary =============================== 645s tests/test_core/test_gpr.py::test_and_gpr[a AND b-2-gpr_genes2-a and b] 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_or_gpr[a OR b-2-gpr_genes2-a or b] 645s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[a OR b-symbolic_gpr2] 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 645s tests/test_core/test_gpr.py::test_gpr_from_symbolic[a OR b-symbolic_gpr5] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_complicated_gpr[(a OR b) AND c] 645s tests/test_core/test_gpr.py::test_gpr_as_symbolic_boolean[(a OR b) AND c-symbolic_gpr6] 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_and_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 645s tests/test_core/test_gpr.py::test_gpr_from_symbolic[(a OR b) AND c-symbolic_gpr9] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule '(a OR b) AND c'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_gpr_that_needs_two_replacements 645s /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)'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_and_b_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists3] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b AND a'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_or_b_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists0] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists6] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'b OR a'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_or_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists1] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists4] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists8] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a OR b or c'. 645s warn( 645s 645s tests/test_core/test_gpr.py::test_gpr_equality_with_bolean_logic[a_b_c_and_strs] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists2] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists5] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists7] 645s tests/test_core/test_gpr.py::test_gpr_inequality_boolean[gpr_lists9] 645s /usr/lib/python3/dist-packages/cobra/core/gene.py:358: SyntaxWarning: Uppercase AND/OR found in rule 'a AND b and c'. 645s warn( 645s 645s tests/test_core/test_model.py::test_reaction_delete 645s tests/test_core/test_model.py::test_reaction_delete 645s /usr/lib/python3/dist-packages/cobra/core/reaction.py:879: DeprecationWarning: delete is deprecated. Use reaction.remove_from_model instead 645s warn( 645s 645s tests/test_core/test_model.py::test_group_loss_of_elements 645s tests/test_flux_analysis/test_gapfilling.py::test_gapfilling 645s /usr/lib/python3/dist-packages/cobra/core/group.py:147: UserWarning: need to pass in a list 645s warn("need to pass in a list") 645s 645s tests/test_core/test_model.py::test_change_objective 645s tests/test_core/test_model.py::test_change_objective 645s tests/test_core/test_model.py::test_change_objective 645s /usr/lib/python3/dist-packages/cobra/core/reaction.py:761: DeprecationWarning: Please use reaction.flux instead. 645s warn("Please use reaction.flux instead.", DeprecationWarning) 645s 645s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 645s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 645s /tmp/autopkgtest.yZCirX/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 645s assert math.isnan(sol.growth) 645s 645s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 645s tests/test_flux_analysis/test_deletion.py::test_double_reaction_deletion 645s /tmp/autopkgtest.yZCirX/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 645s assert math.isnan(sol_one.growth) 645s 645s tests/test_io/test_json.py: 1 warning 645s tests/test_io/test_mat.py: 5 warnings 645s tests/test_io/test_pickle.py: 1 warning 645s tests/test_io/test_sbml.py: 9 warnings 645s tests/test_io/test_yaml.py: 1 warning 645s /usr/lib/python3/dist-packages/cobra/util/solver.py:554: UserWarning: Solver status is 'infeasible'. 645s warn(f"Solver status is '{status}'.", UserWarning) 645s 645s tests/test_io/test_yaml.py::test_save_yaml_model 645s /tmp/autopkgtest.yZCirX/autopkgtest_tmp/tests/test_io/test_yaml.py:29: PendingDeprecationWarning: 645s you should no longer specify 'unsafe'. 645s For **dumping only** use yaml=YAML(typ='full') 645s 645s yaml = YAML(typ="unsafe") 645s 645s tests/test_medium/test_boundary_types.py: 96 warnings 645s /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]` 645s return most[0] 645s 645s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 645s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 645s tests/test_medium/test_boundary_types.py::test_find_external_compartment_multi 645s /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]` 645s compartment = most[matches[most]][0] 645s 645s tests/test_util/test_process_pool.py::test_with_context 645s /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 645s self._pool.__enter__() 645s 645s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 645s 645s ------------------------------------------------------------------------------------------------------------------------ benchmark: 31 tests ------------------------------------------------------------------------------------------------------------------------- 645s Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations 645s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 645s test_subtract_metabolite_benchmark[cplex] 8.9000 (1.0) 226.3110 (3.54) 9.7489 (1.02) 5.5554 (2.32) 9.2250 (1.00) 0.2250 (1.28) 41;166 102,575.7071 (0.98) 2339 1 645s test_subtract_metabolite_benchmark[gurobi] 8.9240 (1.00) 70.3460 (1.10) 9.6394 (1.01) 3.1415 (1.31) 9.1990 (1.0) 0.1760 (1.0) 50;129 103,740.5970 (0.99) 1989 1 645s test_subtract_metabolite_benchmark[glpk] 8.9990 (1.01) 63.9710 (1.0) 9.5840 (1.0) 2.3986 (1.0) 9.2490 (1.01) 0.2240 (1.27) 46;131 104,340.0246 (1.0) 2065 1 645s test_change_objective_benchmark[optlang-glpk] 598.1360 (67.21) 3,010.0290 (47.05) 711.3187 (74.22) 159.9608 (66.69) 674.3340 (73.31) 101.8535 (578.71) 70;54 1,405.8395 (0.01) 2043 1 645s test_achr_sample_benchmark 630.1690 (70.81) 791.8160 (12.38) 677.6739 (70.71) 30.8074 (12.84) 677.1055 (73.61) 43.0495 (244.60) 149;8 1,475.6361 (0.01) 388 1 645s test_optgp_sample_benchmark 964.6890 (108.39) 1,383.9600 (21.63) 1,054.7191 (110.05) 63.5196 (26.48) 1,032.3630 (112.23) 54.1563 (307.71) 85;55 948.1197 (0.01) 649 1 645s test_loopless_benchmark_after 2,790.4420 (313.53) 3,606.3080 (56.37) 2,994.6141 (312.46) 176.0062 (73.38) 2,915.4660 (316.93) 129.1792 (733.97) 34;32 333.9328 (0.00) 155 1 645s test_single_gene_deletion_fba_benchmark[glpk] 11,935.8180 (>1000.0) 14,906.1030 (233.01) 12,677.5964 (>1000.0) 675.7443 (281.73) 12,430.6340 (>1000.0) 918.3690 (>1000.0) 17;2 78.8793 (0.00) 72 1 645s test_loopless_benchmark_before 14,426.6570 (>1000.0) 18,917.1040 (295.71) 15,347.6688 (>1000.0) 1,074.7645 (448.08) 15,020.2010 (>1000.0) 520.1440 (>1000.0) 5;5 65.1565 (0.00) 43 1 645s test_minimal_medium_mip_benchmark 15,888.6540 (>1000.0) 17,133.5410 (267.83) 16,377.1175 (>1000.0) 328.8381 (137.10) 16,312.3625 (>1000.0) 541.7200 (>1000.0) 14;0 61.0608 (0.00) 38 1 645s test_minimal_medium_linear_benchmark 16,081.7270 (>1000.0) 18,291.4790 (285.93) 16,855.7334 (>1000.0) 393.5719 (164.09) 16,836.4065 (>1000.0) 538.9700 (>1000.0) 10;1 59.3270 (0.00) 38 1 645s test_copy_benchmark[optlang-glpk] 42,506.5990 (>1000.0) 50,668.5000 (792.05) 46,296.9661 (>1000.0) 2,509.0708 (>1000.0) 46,484.0275 (>1000.0) 4,309.4410 (>1000.0) 8;0 21.5997 (0.00) 22 1 645s test_flux_variability_loopless_benchmark[glpk] 56,335.1630 (>1000.0) 70,717.8050 (>1000.0) 60,548.4351 (>1000.0) 4,442.4510 (>1000.0) 59,512.4125 (>1000.0) 3,232.4860 (>1000.0) 1;1 16.5157 (0.00) 8 1 645s test_single_reaction_deletion_benchmark[glpk] 67,066.7690 (>1000.0) 69,053.6490 (>1000.0) 68,001.5249 (>1000.0) 528.0258 (220.14) 68,011.8180 (>1000.0) 605.1293 (>1000.0) 5;0 14.7056 (0.00) 15 1 645s test_gpr_equality_benchmark 71,696.1390 (>1000.0) 85,162.2410 (>1000.0) 76,737.5439 (>1000.0) 4,966.7034 (>1000.0) 73,738.9130 (>1000.0) 8,381.9520 (>1000.0) 4;0 13.0314 (0.00) 13 1 645s test_deepcopy_benchmark 74,058.7290 (>1000.0) 85,106.5720 (>1000.0) 80,294.8567 (>1000.0) 3,279.6158 (>1000.0) 80,838.3640 (>1000.0) 5,348.7637 (>1000.0) 4;0 12.4541 (0.00) 13 1 645s test_fastcc_benchmark[glpk] 162,131.8370 (>1000.0) 172,633.9490 (>1000.0) 166,355.2413 (>1000.0) 4,722.6174 (>1000.0) 165,842.3215 (>1000.0) 7,371.0690 (>1000.0) 1;0 6.0112 (0.00) 6 1 645s test_add_metabolite_benchmark[gurobi] 166,533.6850 (>1000.0) 173,199.0920 (>1000.0) 169,372.3587 (>1000.0) 2,756.1333 (>1000.0) 168,261.6220 (>1000.0) 4,972.8670 (>1000.0) 3;0 5.9042 (0.00) 7 1 645s test_add_metabolite_benchmark[glpk] 171,408.0170 (>1000.0) 221,173.7920 (>1000.0) 183,918.5410 (>1000.0) 18,262.0260 (>1000.0) 174,635.9960 (>1000.0) 16,692.4835 (>1000.0) 1;1 5.4372 (0.00) 7 1 645s test_add_metabolite_benchmark[cplex] 172,213.4390 (>1000.0) 225,362.1940 (>1000.0) 186,284.2836 (>1000.0) 18,822.0589 (>1000.0) 176,711.9050 (>1000.0) 15,820.6572 (>1000.0) 1;1 5.3681 (0.00) 7 1 645s test_optgp_init_benchmark 226,387.2690 (>1000.0) 248,365.9340 (>1000.0) 234,706.5204 (>1000.0) 8,989.1402 (>1000.0) 230,583.4500 (>1000.0) 12,971.2805 (>1000.0) 1;0 4.2606 (0.00) 5 1 645s test_achr_init_benchmark 230,605.8730 (>1000.0) 261,152.6200 (>1000.0) 243,552.1192 (>1000.0) 12,019.3766 (>1000.0) 239,803.5000 (>1000.0) 17,473.7880 (>1000.0) 2;0 4.1059 (0.00) 5 1 645s test_double_reaction_deletion_benchmark 265,018.1340 (>1000.0) 271,847.2660 (>1000.0) 267,295.9766 (>1000.0) 2,659.5927 (>1000.0) 266,313.6180 (>1000.0) 2,523.6798 (>1000.0) 1;0 3.7412 (0.00) 5 1 645s test_single_gene_deletion_linear_moma_benchmark[glpk] 499,583.9780 (>1000.0) 531,387.8230 (>1000.0) 511,874.9242 (>1000.0) 13,621.5798 (>1000.0) 506,087.6400 (>1000.0) 22,016.1057 (>1000.0) 1;0 1.9536 (0.00) 5 1 645s test_gpr_symbolism_benchmark 537,195.7430 (>1000.0) 557,656.7530 (>1000.0) 544,640.2134 (>1000.0) 9,528.0726 (>1000.0) 538,173.0920 (>1000.0) 15,510.9132 (>1000.0) 1;0 1.8361 (0.00) 5 1 645s test_single_gene_deletion_linear_room_benchmark[glpk] 727,281.4230 (>1000.0) 1,344,580.8930 (>1000.0) 861,890.9618 (>1000.0) 269,998.2725 (>1000.0) 749,435.5530 (>1000.0) 163,881.7425 (>1000.0) 1;1 1.1602 (0.00) 5 1 645s test_pfba_benchmark[glpk] 734,953.5510 (>1000.0) 1,312,500.7570 (>1000.0) 854,947.5884 (>1000.0) 255,811.2634 (>1000.0) 740,684.1310 (>1000.0) 148,826.6777 (>1000.0) 1;1 1.1697 (0.00) 5 1 645s test_double_gene_deletion_benchmark 739,032.1970 (>1000.0) 752,569.4760 (>1000.0) 744,924.7368 (>1000.0) 4,991.5835 (>1000.0) 744,400.1860 (>1000.0) 5,865.1870 (>1000.0) 2;0 1.3424 (0.00) 5 1 645s test_copy_benchmark_large_model[optlang-glpk] 956,158.7640 (>1000.0) 1,923,024.8460 (>1000.0) 1,360,347.6210 (>1000.0) 481,002.4252 (>1000.0) 1,087,136.6450 (>1000.0) 881,861.7660 (>1000.0) 2;0 0.7351 (0.00) 5 1 645s test_geometric_fba_benchmark[glpk] 1,066,338.9940 (>1000.0) 1,568,592.6720 (>1000.0) 1,168,947.1312 (>1000.0) 223,418.4795 (>1000.0) 1,068,845.2230 (>1000.0) 128,181.5982 (>1000.0) 1;1 0.8555 (0.00) 5 1 645s test_flux_variability_benchmark[glpk] 1,375,060.2240 (>1000.0) 1,388,944.9780 (>1000.0) 1,381,836.8332 (>1000.0) 5,189.6374 (>1000.0) 1,382,311.9660 (>1000.0) 6,945.5725 (>1000.0) 2;0 0.7237 (0.00) 5 1 645s ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 645s 645s Legend: 645s Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. 645s OPS: Operations Per Second, computed as 1 / Mean 645s = 513 passed, 27 skipped, 10 xfailed, 1 xpassed, 172 warnings in 275.70s (0:04:35) = 648s Removing patch debian/patches/no_future_dependency.patch 648s Restoring setup.cfg 648s 648s Removing patch debian/patches/32-bit-test.patch 648s Restoring tests/test_io/test_mat.py 648s 648s Removing patch debian/patches/do-not-seek-for-name.patch 648s Restoring src/cobra/io/sbml.py 648s 648s Removing patch debian/patches/ignore_tests.patch 648s Restoring tests/test_io/test_web/test_load.py 649s 649s Removing patch debian/patches/xfail_test_show_versions.patch 649s Restoring tests/test_util/test_util.py 649s 649s Removing patch debian/patches/mathjax.patch 649s Restoring documentation_builder/conf.py 649s 649s No patches applied 649s PASS 649s autopkgtest [06:51:16]: test run-unit-test: -----------------------] 650s autopkgtest [06:51:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 650s run-unit-test PASS 650s autopkgtest [06:51:17]: @@@@@@@@@@@@@@@@@@@@ summary 650s run-unit-test PASS 722s Creating nova instance adt-oracular-arm64-python-cobra-20240505-064027-juju-7f2275-prod-proposed-migration-environment-2-1fddf9e0-a22b-42df-9ee1-ce4f21ae9ae8 from image adt/ubuntu-oracular-arm64-server-20240503.img (UUID d6f0a588-bf5e-4a78-b5df-9ca1fb1dc89e)...