0s autopkgtest [15:44:13]: starting date and time: 2025-10-20 15:44:13+0000 0s autopkgtest [15:44:13]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:44:13]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hdx__n_l/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-9.secgroup --name adt-resolute-s390x-gemmi-20251020-154413-juju-7f2275-prod-proposed-migration-environment-15-b424448c-2680-44ab-8535-7dafc5546fd4 --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/ 4s Creating nova instance adt-resolute-s390x-gemmi-20251020-154413-juju-7f2275-prod-proposed-migration-environment-15-b424448c-2680-44ab-8535-7dafc5546fd4 from image adt/ubuntu-resolute-s390x-server-20251020.img (UUID af6042e7-5f94-4102-8fd4-5557e2338897)... 40s autopkgtest [15:44:53]: testbed dpkg architecture: s390x 40s autopkgtest [15:44:53]: testbed apt version: 3.1.8ubuntu1 40s autopkgtest [15:44:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 40s autopkgtest [15:44:53]: testbed release detected to be: None 41s autopkgtest [15:44:54]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 41s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 41s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 42s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 42s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 42s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 42s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [56.9 kB] 42s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 42s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 42s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 42s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [400 kB] 42s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 42s Fetched 1318 kB in 1s (1343 kB/s) 43s Reading package lists... 43s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 43s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 43s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 44s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 44s Reading package lists... 44s Reading package lists... 44s Building dependency tree... 44s Reading state information... 44s Calculating upgrade... 45s The following packages will be upgraded: 45s libjson-c5 python3-inflect python3-oauthlib python3-zipp 45s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 45s Need to get 175 kB of archives. 45s After this operation, 31.7 kB of additional disk space will be used. 45s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-c5 s390x 0.18+ds-1.1 [36.8 kB] 45s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-inflect all 7.5.0-1 [33.9 kB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-oauthlib all 3.3.1-1 [93.5 kB] 45s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-zipp all 3.23.0-1 [10.4 kB] 45s dpkg-preconfigure: unable to re-open stdin: No such file or directory 45s Fetched 175 kB in 0s (431 kB/s) 45s (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 ... 56857 files and directories currently installed.) 45s Preparing to unpack .../libjson-c5_0.18+ds-1.1_s390x.deb ... 45s Unpacking libjson-c5:s390x (0.18+ds-1.1) over (0.18+ds-1) ... 45s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 45s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 45s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 45s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 46s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 46s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 46s Setting up python3-zipp (3.23.0-1) ... 46s Setting up python3-inflect (7.5.0-1) ... 46s Setting up python3-oauthlib (3.3.1-1) ... 46s Setting up libjson-c5:s390x (0.18+ds-1.1) ... 46s Processing triggers for libc-bin (2.42-0ubuntu3) ... 46s autopkgtest [15:44:59]: upgrading testbed (apt dist-upgrade and autopurge) 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 46s Calculating upgrade... 47s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 47s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Solving dependencies... 47s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 49s autopkgtest [15:45:02]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 50s autopkgtest [15:45:03]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 52s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (dsc) [2280 B] 52s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (tar) [1290 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (diff) [7464 B] 52s gpgv: Signature made Mon Feb 3 14:50:02 2025 UTC 52s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 52s gpgv: issuer "merkys@debian.org" 52s gpgv: Can't check signature: No public key 52s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: no acceptable signature found 53s autopkgtest [15:45:06]: testing package gemmi version 0.6.5+ds-3 53s autopkgtest [15:45:06]: build not needed 54s autopkgtest [15:45:07]: test command1: preparing testbed 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Solving dependencies... 54s The following NEW packages will be installed: 54s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 54s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 54s python3-pluggy python3-pytest tao-pegtl-dev 55s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 13.6 MB of archives. 55s After this operation, 53.3 MB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 55s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 55s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 55s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x gemmi s390x 0.6.5+ds-3 [1186 kB] 59s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x tao-pegtl-dev all 3.2.7-1 [59.6 kB] 59s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x gemmi-dev s390x 0.6.5+ds-3 [1274 kB] 59s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gemmi s390x 0.6.5+ds-3 [2368 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 60s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 60s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pytest all 8.4.2-1 [268 kB] 60s Fetched 13.6 MB in 5s (2531 kB/s) 60s Selecting previously unselected package python3-numpy-dev:s390x. 60s (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 ... 56867 files and directories currently installed.) 60s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 60s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 60s Selecting previously unselected package libblas3:s390x. 60s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 60s Unpacking libblas3:s390x (3.12.1-6build1) ... 60s Selecting previously unselected package libgfortran5:s390x. 60s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 60s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 60s Selecting previously unselected package liblapack3:s390x. 60s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 60s Unpacking liblapack3:s390x (3.12.1-6build1) ... 60s Selecting previously unselected package python3-numpy. 60s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 60s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 60s Selecting previously unselected package gemmi. 60s Preparing to unpack .../05-gemmi_0.6.5+ds-3_s390x.deb ... 60s Unpacking gemmi (0.6.5+ds-3) ... 60s Selecting previously unselected package tao-pegtl-dev. 60s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 60s Unpacking tao-pegtl-dev (3.2.7-1) ... 60s Selecting previously unselected package gemmi-dev. 60s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_s390x.deb ... 60s Unpacking gemmi-dev (0.6.5+ds-3) ... 60s Selecting previously unselected package python3-gemmi. 60s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_s390x.deb ... 60s Unpacking python3-gemmi (0.6.5+ds-3) ... 60s Selecting previously unselected package python3-iniconfig. 60s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 60s Unpacking python3-iniconfig (1.1.1-2) ... 60s Selecting previously unselected package python3-packaging. 60s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 60s Unpacking python3-packaging (25.0-1) ... 60s Selecting previously unselected package python3-pluggy. 60s Preparing to unpack .../11-python3-pluggy_1.6.0-1_all.deb ... 60s Unpacking python3-pluggy (1.6.0-1) ... 60s Selecting previously unselected package python3-pytest. 60s Preparing to unpack .../12-python3-pytest_8.4.2-1_all.deb ... 60s Unpacking python3-pytest (8.4.2-1) ... 60s Setting up python3-iniconfig (1.1.1-2) ... 61s Setting up python3-gemmi (0.6.5+ds-3) ... 61s Setting up libblas3:s390x (3.12.1-6build1) ... 61s 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 61s Setting up python3-packaging (25.0-1) ... 61s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 61s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 61s Setting up python3-pluggy (1.6.0-1) ... 61s Setting up gemmi (0.6.5+ds-3) ... 61s Setting up tao-pegtl-dev (3.2.7-1) ... 61s Setting up liblapack3:s390x (3.12.1-6build1) ... 61s 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 61s Setting up python3-pytest (8.4.2-1) ... 61s Setting up gemmi-dev (0.6.5+ds-3) ... 61s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 62s Processing triggers for man-db (2.13.1-1) ... 63s Processing triggers for libc-bin (2.42-0ubuntu3) ... 64s autopkgtest [15:45:17]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 64s autopkgtest [15:45:17]: test command1: [----------------------- 65s ........................................................................ [ 38%] 65s .............................s.................s..............ssssss.... [ 76%] 65s ............................................ [100%] 65s =========================== short test summary info ============================ 65s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 65s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 65s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 65s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 65s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 65s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 65s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 65s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 65s 180 passed, 8 skipped, 3 deselected in 0.76s 66s autopkgtest [15:45:19]: test command1: -----------------------] 66s autopkgtest [15:45:19]: test command1: - - - - - - - - - - results - - - - - - - - - - 66s command1 PASS 67s autopkgtest [15:45:20]: @@@@@@@@@@@@@@@@@@@@ summary 67s command1 PASS