0s autopkgtest [20:04:20]: starting date and time: 2025-10-20 20:04:20+0000 0s autopkgtest [20:04:20]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:04:20]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f0jzbxt3/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-11.secgroup --name adt-resolute-arm64-gemmi-20251020-200420-juju-7f2275-prod-proposed-migration-environment-15-66c913be-589c-4417-9fc9-059596fd9464 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-gemmi-20251020-200420-juju-7f2275-prod-proposed-migration-environment-15-66c913be-589c-4417-9fc9-059596fd9464 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 58s autopkgtest [20:05:18]: testbed dpkg architecture: arm64 58s autopkgtest [20:05:18]: testbed apt version: 3.1.8ubuntu1 59s autopkgtest [20:05:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 59s autopkgtest [20:05:19]: testbed release detected to be: None 60s autopkgtest [20:05:20]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 60s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 60s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 61s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 61s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 61s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 61s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 61s Fetched 1382 kB in 1s (1369 kB/s) 62s Reading package lists... 62s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 63s 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 64s Reading package lists... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Calculating upgrade... 65s The following packages will be upgraded: 65s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 65s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Need to get 512 kB of archives. 65s After this operation, 31.7 kB of additional disk space will be used. 65s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 65s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 65s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 65s dpkg-preconfigure: unable to re-open stdin: No such file or directory 66s Fetched 512 kB in 1s (899 kB/s) 66s (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 ... 83364 files and directories currently installed.) 66s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 66s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 66s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 66s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 66s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 66s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 66s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 66s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 66s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 66s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 66s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 66s Setting up python3-zipp (3.23.0-1) ... 67s Setting up python3-inflect (7.5.0-1) ... 67s Setting up python3-oauthlib (3.3.1-1) ... 67s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 67s Processing triggers for libc-bin (2.42-0ubuntu3) ... 67s autopkgtest [20:05:27]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Solving dependencies... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s autopkgtest [20:05:32]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 72s autopkgtest [20:05:32]: @@@@@@@@@@@@@@@@@@@@ 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 76s autopkgtest [20:05:36]: testing package gemmi version 0.6.5+ds-3 76s autopkgtest [20:05:36]: build not needed 77s autopkgtest [20:05:37]: test command1: preparing testbed 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Solving dependencies... 78s The following NEW packages will be installed: 78s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 78s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 78s python3-pluggy python3-pytest tao-pegtl-dev 78s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 12.0 MB of archives. 78s After this operation, 48.1 MB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 79s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 gemmi arm64 0.6.5+ds-3 [1069 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 tao-pegtl-dev all 3.2.7-1 [59.6 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 gemmi-dev arm64 0.6.5+ds-3 [1203 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gemmi arm64 0.6.5+ds-3 [2206 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 81s Fetched 12.0 MB in 2s (4901 kB/s) 81s Selecting previously unselected package python3-numpy-dev:arm64. 81s (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 ... 83374 files and directories currently installed.) 81s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 81s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 81s Selecting previously unselected package libblas3:arm64. 81s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 81s Unpacking libblas3:arm64 (3.12.1-6build1) ... 81s Selecting previously unselected package libgfortran5:arm64. 81s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 81s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 81s Selecting previously unselected package liblapack3:arm64. 81s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 81s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 81s Selecting previously unselected package python3-numpy. 81s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 81s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 81s Selecting previously unselected package gemmi. 81s Preparing to unpack .../05-gemmi_0.6.5+ds-3_arm64.deb ... 81s Unpacking gemmi (0.6.5+ds-3) ... 81s Selecting previously unselected package tao-pegtl-dev. 81s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 81s Unpacking tao-pegtl-dev (3.2.7-1) ... 81s Selecting previously unselected package gemmi-dev. 81s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_arm64.deb ... 81s Unpacking gemmi-dev (0.6.5+ds-3) ... 81s Selecting previously unselected package python3-gemmi. 81s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_arm64.deb ... 81s Unpacking python3-gemmi (0.6.5+ds-3) ... 82s Selecting previously unselected package python3-iniconfig. 82s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 82s Unpacking python3-iniconfig (1.1.1-2) ... 82s Selecting previously unselected package python3-packaging. 82s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 82s Unpacking python3-packaging (25.0-1) ... 82s Selecting previously unselected package python3-pluggy. 82s Preparing to unpack .../11-python3-pluggy_1.6.0-1_all.deb ... 82s Unpacking python3-pluggy (1.6.0-1) ... 82s Selecting previously unselected package python3-pytest. 82s Preparing to unpack .../12-python3-pytest_8.4.2-1_all.deb ... 82s Unpacking python3-pytest (8.4.2-1) ... 82s Setting up python3-iniconfig (1.1.1-2) ... 82s Setting up python3-gemmi (0.6.5+ds-3) ... 82s Setting up libblas3:arm64 (3.12.1-6build1) ... 82s 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 82s Setting up python3-packaging (25.0-1) ... 82s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 82s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 82s Setting up python3-pluggy (1.6.0-1) ... 82s Setting up gemmi (0.6.5+ds-3) ... 82s Setting up tao-pegtl-dev (3.2.7-1) ... 82s Setting up liblapack3:arm64 (3.12.1-6build1) ... 82s 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 82s Setting up python3-pytest (8.4.2-1) ... 83s Setting up gemmi-dev (0.6.5+ds-3) ... 83s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 85s Processing triggers for man-db (2.13.1-1) ... 85s Processing triggers for libc-bin (2.42-0ubuntu3) ... 87s autopkgtest [20:05:47]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 87s autopkgtest [20:05:47]: test command1: [----------------------- 88s ........................................................................ [ 38%] 88s .............................s.................s..............ssssss.... [ 76%] 89s ............................................ [100%] 89s =========================== short test summary info ============================ 89s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 89s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 89s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 89s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 89s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 89s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 89s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 89s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 89s 180 passed, 8 skipped, 3 deselected in 1.15s 89s autopkgtest [20:05:49]: test command1: -----------------------] 90s command1 PASS 90s autopkgtest [20:05:50]: test command1: - - - - - - - - - - results - - - - - - - - - - 90s autopkgtest [20:05:50]: @@@@@@@@@@@@@@@@@@@@ summary 90s command1 PASS