0s autopkgtest [18:21:23]: starting date and time: 2025-10-18 18:21:23+0000 0s autopkgtest [18:21:23]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [18:21:23]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xcrcugan/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-3.secgroup --name adt-resolute-s390x-gemmi-20251018-182122-juju-7f2275-prod-proposed-migration-environment-15-449284c8-ff89-4d3e-980e-a2e5802a06ae --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-gemmi-20251018-182122-juju-7f2275-prod-proposed-migration-environment-15-449284c8-ff89-4d3e-980e-a2e5802a06ae from image adt/ubuntu-resolute-s390x-server-20251018.img (UUID c47ab411-f9be-46ce-b861-20d934d06dba)... 45s autopkgtest [18:22:08]: testbed dpkg architecture: s390x 46s autopkgtest [18:22:09]: testbed apt version: 3.1.6ubuntu2 46s autopkgtest [18:22:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s autopkgtest [18:22:09]: testbed release detected to be: None 47s autopkgtest [18:22:10]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [456 kB] 48s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 48s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [50.7 kB] 48s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [16.7 kB] 48s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [92.8 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 48s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [314 kB] 48s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [4660 B] 48s Fetched 1023 kB in 1s (889 kB/s) 49s Reading package lists... 50s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 50s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 50s Reading package lists... 50s Reading package lists... 51s Building dependency tree... 51s Reading state information... 51s Calculating upgrade... 51s The following packages will be upgraded: 51s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 51s libpython3-stdlib lto-disabled-list python3 python3-minimal 51s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 2763 kB of archives. 51s After this operation, 14.3 kB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 51s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 51s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 51s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libapt-pkg7.0 s390x 3.1.8ubuntu1 [1144 kB] 51s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x apt s390x 3.1.8ubuntu1 [1432 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libgirepository-1.0-1 s390x 1.86.0-6 [86.9 kB] 52s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x gir1.2-girepository-2.0 s390x 1.86.0-6 [25.1 kB] 52s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x lto-disabled-list all 71 [12.5 kB] 52s dpkg-preconfigure: unable to re-open stdin: No such file or directory 52s Fetched 2763 kB in 1s (3026 kB/s) 52s (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 ... 56852 files and directories currently installed.) 52s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 52s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 52s Setting up python3-minimal (3.13.7-2) ... 52s (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 ... 56852 files and directories currently installed.) 52s Preparing to unpack .../0-python3_3.13.7-2_s390x.deb ... 52s running python pre-rtupdate hooks for python3.13... 52s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 52s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_s390x.deb ... 52s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 52s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_s390x.deb ... 52s Unpacking libapt-pkg7.0:s390x (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 52s Preparing to unpack .../3-apt_3.1.8ubuntu1_s390x.deb ... 52s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 52s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_s390x.deb ... 52s Unpacking libgirepository-1.0-1:s390x (1.86.0-6) over (1.84.0-1) ... 52s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_s390x.deb ... 52s Unpacking gir1.2-girepository-2.0:s390x (1.86.0-6) over (1.84.0-1) ... 52s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 52s Unpacking lto-disabled-list (71) over (69) ... 53s Setting up lto-disabled-list (71) ... 53s Setting up libgirepository-1.0-1:s390x (1.86.0-6) ... 53s Setting up libapt-pkg7.0:s390x (3.1.8ubuntu1) ... 53s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 53s Setting up apt (3.1.8ubuntu1) ... 53s Setting up python3 (3.13.7-2) ... 53s running python rtupdate hooks for python3.13... 53s running python post-rtupdate hooks for python3.13... 53s Setting up gir1.2-girepository-2.0:s390x (1.86.0-6) ... 53s Processing triggers for man-db (2.13.1-1) ... 54s Processing triggers for libc-bin (2.42-0ubuntu3) ... 54s autopkgtest [18:22:17]: upgrading testbed (apt dist-upgrade and autopurge) 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Solving dependencies... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s autopkgtest [18:22:19]: rebooting testbed after setup commands that affected boot 69s autopkgtest [18:22:32]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 72s autopkgtest [18:22:35]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 75s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (dsc) [2280 B] 75s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (tar) [1290 kB] 75s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (diff) [7464 B] 75s gpgv: Signature made Mon Feb 3 14:50:02 2025 UTC 75s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 75s gpgv: issuer "merkys@debian.org" 75s gpgv: Can't check signature: No public key 75s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: no acceptable signature found 75s autopkgtest [18:22:38]: testing package gemmi version 0.6.5+ds-3 76s autopkgtest [18:22:39]: build not needed 77s autopkgtest [18:22:40]: test command1: preparing testbed 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Solving dependencies... 77s The following NEW packages will be installed: 77s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 77s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 77s python3-pluggy python3-pytest tao-pegtl-dev 77s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 13.6 MB of archives. 77s After this operation, 53.2 MB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 78s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 78s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 79s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x gemmi s390x 0.6.5+ds-3 [1186 kB] 79s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x tao-pegtl-dev all 3.2.7-1 [59.6 kB] 79s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x gemmi-dev s390x 0.6.5+ds-3 [1274 kB] 79s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gemmi s390x 0.6.5+ds-3 [2368 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 8.3.5-2 [252 kB] 80s Fetched 13.6 MB in 3s (5266 kB/s) 80s Selecting previously unselected package python3-numpy-dev:s390x. 80s (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 ... 56852 files and directories currently installed.) 80s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 80s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 80s Selecting previously unselected package libblas3:s390x. 80s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 80s Unpacking libblas3:s390x (3.12.1-6build1) ... 80s Selecting previously unselected package libgfortran5:s390x. 80s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 80s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 80s Selecting previously unselected package liblapack3:s390x. 80s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 80s Unpacking liblapack3:s390x (3.12.1-6build1) ... 80s Selecting previously unselected package python3-numpy. 80s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 80s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 80s Selecting previously unselected package gemmi. 80s Preparing to unpack .../05-gemmi_0.6.5+ds-3_s390x.deb ... 80s Unpacking gemmi (0.6.5+ds-3) ... 80s Selecting previously unselected package tao-pegtl-dev. 80s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 80s Unpacking tao-pegtl-dev (3.2.7-1) ... 80s Selecting previously unselected package gemmi-dev. 80s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_s390x.deb ... 80s Unpacking gemmi-dev (0.6.5+ds-3) ... 80s Selecting previously unselected package python3-gemmi. 80s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_s390x.deb ... 80s Unpacking python3-gemmi (0.6.5+ds-3) ... 80s Selecting previously unselected package python3-iniconfig. 80s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 80s Unpacking python3-iniconfig (1.1.1-2) ... 80s Selecting previously unselected package python3-packaging. 80s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 80s Unpacking python3-packaging (25.0-1) ... 80s Selecting previously unselected package python3-pluggy. 80s Preparing to unpack .../11-python3-pluggy_1.5.0-1_all.deb ... 80s Unpacking python3-pluggy (1.5.0-1) ... 80s Selecting previously unselected package python3-pytest. 80s Preparing to unpack .../12-python3-pytest_8.3.5-2_all.deb ... 80s Unpacking python3-pytest (8.3.5-2) ... 80s Setting up python3-iniconfig (1.1.1-2) ... 80s Setting up python3-gemmi (0.6.5+ds-3) ... 81s Setting up libblas3:s390x (3.12.1-6build1) ... 81s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 81s Setting up python3-packaging (25.0-1) ... 81s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 81s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 81s Setting up python3-pluggy (1.5.0-1) ... 81s Setting up gemmi (0.6.5+ds-3) ... 81s Setting up tao-pegtl-dev (3.2.7-1) ... 81s Setting up liblapack3:s390x (3.12.1-6build1) ... 81s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 81s Setting up python3-pytest (8.3.5-2) ... 81s Setting up gemmi-dev (0.6.5+ds-3) ... 81s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 82s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for libc-bin (2.42-0ubuntu3) ... 84s autopkgtest [18:22:47]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 84s autopkgtest [18:22:47]: test command1: [----------------------- 85s ........................................................................ [ 38%] 85s .............................s.................s..............ssssss.... [ 76%] 85s ............................................ [100%] 85s =========================== short test summary info ============================ 85s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 85s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 85s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 85s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 85s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 85s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 85s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 85s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 85s 180 passed, 8 skipped, 3 deselected in 0.75s 85s autopkgtest [18:22:48]: test command1: -----------------------] 86s command1 PASS 86s autopkgtest [18:22:49]: test command1: - - - - - - - - - - results - - - - - - - - - - 86s autopkgtest [18:22:49]: @@@@@@@@@@@@@@@@@@@@ summary 86s command1 PASS