0s autopkgtest [19:05:01]: starting date and time: 2025-10-18 19:05:01+0000 0s autopkgtest [19:05:01]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:05:01]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bfvwn4_f/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-3.secgroup --name adt-resolute-ppc64el-gemmi-20251018-190500-juju-7f2275-prod-proposed-migration-environment-15-731f64d3-ae4e-4856-b7ab-f40bd2b933aa --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-gemmi-20251018-190500-juju-7f2275-prod-proposed-migration-environment-15-731f64d3-ae4e-4856-b7ab-f40bd2b933aa from image adt/ubuntu-resolute-ppc64el-server-20251018.img (UUID 746a0a80-14f1-4bf7-89b6-cbb5ab236a4e)... 60s autopkgtest [19:06:01]: testbed dpkg architecture: ppc64el 60s autopkgtest [19:06:01]: testbed apt version: 3.1.8ubuntu1 61s autopkgtest [19:06:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s autopkgtest [19:06:02]: testbed release detected to be: None 62s autopkgtest [19:06:03]: updating testbed package index (apt update) 62s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 62s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [50.7 kB] 63s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [456 kB] 63s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 63s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [16.7 kB] 64s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [92.0 kB] 64s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 64s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [317 kB] 64s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4660 B] 64s Fetched 1026 kB in 2s (457 kB/s) 65s Reading package lists... 66s Failed to check for VM: Permission denied 66s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s The following packages will be upgraded: 67s gir1.2-girepository-2.0 libgirepository-1.0-1 libpython3-stdlib python3 67s python3-minimal 67s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 185 kB of archives. 67s After this operation, 2048 B of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3-minimal ppc64el 3.13.7-2 [27.8 kB] 68s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el python3 ppc64el 3.13.7-2 [23.9 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.7-2 [10.6 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgirepository-1.0-1 ppc64el 1.86.0-6 [97.4 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el gir1.2-girepository-2.0 ppc64el 1.86.0-6 [25.3 kB] 68s dpkg-preconfigure: unable to re-open stdin: No such file or directory 68s Fetched 185 kB in 1s (317 kB/s) 69s (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 ... 76461 files and directories currently installed.) 69s Preparing to unpack .../python3-minimal_3.13.7-2_ppc64el.deb ... 69s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 69s Setting up python3-minimal (3.13.7-2) ... 69s (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 ... 76461 files and directories currently installed.) 69s Preparing to unpack .../python3_3.13.7-2_ppc64el.deb ... 69s running python pre-rtupdate hooks for python3.13... 69s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 70s Preparing to unpack .../libpython3-stdlib_3.13.7-2_ppc64el.deb ... 70s Unpacking libpython3-stdlib:ppc64el (3.13.7-2) over (3.13.7-1) ... 70s Preparing to unpack .../libgirepository-1.0-1_1.86.0-6_ppc64el.deb ... 70s Unpacking libgirepository-1.0-1:ppc64el (1.86.0-6) over (1.84.0-1) ... 70s Preparing to unpack .../gir1.2-girepository-2.0_1.86.0-6_ppc64el.deb ... 70s Unpacking gir1.2-girepository-2.0:ppc64el (1.86.0-6) over (1.84.0-1) ... 70s Setting up libgirepository-1.0-1:ppc64el (1.86.0-6) ... 70s Setting up libpython3-stdlib:ppc64el (3.13.7-2) ... 70s Setting up python3 (3.13.7-2) ... 70s running python rtupdate hooks for python3.13... 70s running python post-rtupdate hooks for python3.13... 70s Setting up gir1.2-girepository-2.0:ppc64el (1.86.0-6) ... 70s Processing triggers for man-db (2.13.1-1) ... 71s Processing triggers for libc-bin (2.42-0ubuntu3) ... 71s autopkgtest [19:06:12]: upgrading testbed (apt dist-upgrade and autopurge) 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Calculating upgrade... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Solving dependencies... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [19:06:16]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 75s autopkgtest [19:06:16]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 79s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (dsc) [2280 B] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (tar) [1290 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (diff) [7464 B] 80s gpgv: Signature made Mon Feb 3 14:50:02 2025 UTC 80s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 80s gpgv: issuer "merkys@debian.org" 80s gpgv: Can't check signature: No public key 80s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: no acceptable signature found 80s autopkgtest [19:06:21]: testing package gemmi version 0.6.5+ds-3 80s autopkgtest [19:06:21]: build not needed 81s autopkgtest [19:06:22]: test command1: preparing testbed 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 82s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 82s python3-pluggy python3-pytest tao-pegtl-dev 82s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 14.6 MB of archives. 82s After this operation, 59.4 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 83s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 84s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el gemmi ppc64el 0.6.5+ds-3 [1353 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el tao-pegtl-dev all 3.2.7-1 [59.6 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el gemmi-dev ppc64el 0.6.5+ds-3 [1336 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-gemmi ppc64el 0.6.5+ds-3 [2613 kB] 86s Get:10 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 86s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 86s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 86s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest all 8.3.5-2 [252 kB] 86s Fetched 14.6 MB in 4s (3419 kB/s) 86s Selecting previously unselected package python3-numpy-dev:ppc64el. 86s (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 ... 76461 files and directories currently installed.) 86s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 86s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 86s Selecting previously unselected package libblas3:ppc64el. 86s Preparing to unpack .../01-libblas3_3.12.1-6build1_ppc64el.deb ... 86s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 86s Selecting previously unselected package libgfortran5:ppc64el. 86s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 86s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 86s Selecting previously unselected package liblapack3:ppc64el. 86s Preparing to unpack .../03-liblapack3_3.12.1-6build1_ppc64el.deb ... 86s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 86s Selecting previously unselected package python3-numpy. 86s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 86s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 87s Selecting previously unselected package gemmi. 87s Preparing to unpack .../05-gemmi_0.6.5+ds-3_ppc64el.deb ... 87s Unpacking gemmi (0.6.5+ds-3) ... 87s Selecting previously unselected package tao-pegtl-dev. 87s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 87s Unpacking tao-pegtl-dev (3.2.7-1) ... 87s Selecting previously unselected package gemmi-dev. 87s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_ppc64el.deb ... 87s Unpacking gemmi-dev (0.6.5+ds-3) ... 87s Selecting previously unselected package python3-gemmi. 87s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_ppc64el.deb ... 87s Unpacking python3-gemmi (0.6.5+ds-3) ... 87s Selecting previously unselected package python3-iniconfig. 87s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 87s Unpacking python3-iniconfig (1.1.1-2) ... 87s Selecting previously unselected package python3-packaging. 87s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 87s Unpacking python3-packaging (25.0-1) ... 87s Selecting previously unselected package python3-pluggy. 87s Preparing to unpack .../11-python3-pluggy_1.5.0-1_all.deb ... 87s Unpacking python3-pluggy (1.5.0-1) ... 87s Selecting previously unselected package python3-pytest. 87s Preparing to unpack .../12-python3-pytest_8.3.5-2_all.deb ... 87s Unpacking python3-pytest (8.3.5-2) ... 87s Setting up python3-iniconfig (1.1.1-2) ... 87s Setting up python3-gemmi (0.6.5+ds-3) ... 87s Setting up libblas3:ppc64el (3.12.1-6build1) ... 87s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 87s Setting up python3-packaging (25.0-1) ... 87s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 87s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 87s Setting up python3-pluggy (1.5.0-1) ... 88s Setting up gemmi (0.6.5+ds-3) ... 88s Setting up tao-pegtl-dev (3.2.7-1) ... 88s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 88s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 88s Setting up python3-pytest (8.3.5-2) ... 88s Setting up gemmi-dev (0.6.5+ds-3) ... 88s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 90s Processing triggers for man-db (2.13.1-1) ... 90s Processing triggers for libc-bin (2.42-0ubuntu3) ... 91s autopkgtest [19:06:32]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 91s autopkgtest [19:06:32]: test command1: [----------------------- 93s ........................................................................ [ 38%] 93s .............................s.................s..............ssssss.... [ 76%] 93s ............................................ [100%] 93s =========================== short test summary info ============================ 93s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 93s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 93s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 93s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 93s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 93s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 93s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 93s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 93s 180 passed, 8 skipped, 3 deselected in 1.06s 93s autopkgtest [19:06:34]: test command1: -----------------------] 94s autopkgtest [19:06:35]: test command1: - - - - - - - - - - results - - - - - - - - - - 94s command1 PASS 94s autopkgtest [19:06:35]: @@@@@@@@@@@@@@@@@@@@ summary 94s command1 PASS