0s autopkgtest [22:26:03]: starting date and time: 2025-10-18 22:26:03+0000 0s autopkgtest [22:26:03]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:26:03]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v103ps2f/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-3.secgroup --name adt-resolute-amd64-gemmi-20251018-222602-juju-7f2275-prod-proposed-migration-environment-15-da4c48f1-0238-4784-a17d-ea87fe3d48e2 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-gemmi-20251018-222602-juju-7f2275-prod-proposed-migration-environment-15-da4c48f1-0238-4784-a17d-ea87fe3d48e2 from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID 1e43d7d4-3f39-4b59-975d-5a285d0b86c1)... 66s autopkgtest [22:27:09]: testbed dpkg architecture: amd64 66s autopkgtest [22:27:09]: testbed apt version: 3.1.6ubuntu2 67s autopkgtest [22:27:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s autopkgtest [22:27:10]: testbed release detected to be: None 67s autopkgtest [22:27:10]: updating testbed package index (apt update) 68s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 68s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 68s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 68s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [431 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [18.2 kB] 69s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 69s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [54.3 kB] 69s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [65.5 kB] 69s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [108 kB] 69s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 69s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 69s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [319 kB] 69s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [125 kB] 69s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3088 B] 69s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [9188 B] 69s Fetched 1253 kB in 1s (1290 kB/s) 69s Reading package lists... 70s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 71s Reading package lists... 71s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Calculating upgrade... 72s The following packages will be upgraded: 72s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 72s libpython3-stdlib lto-disabled-list python3 python3-minimal 72s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 2763 kB of archives. 72s After this operation, 2048 B of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 72s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 72s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 73s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 73s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 73s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 73s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 lto-disabled-list all 71 [12.5 kB] 73s dpkg-preconfigure: unable to re-open stdin: No such file or directory 73s Fetched 2763 kB in 1s (3002 kB/s) 74s (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 ... 78439 files and directories currently installed.) 74s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 74s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 74s Setting up python3-minimal (3.13.7-2) ... 74s (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 ... 78439 files and directories currently installed.) 74s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 74s running python pre-rtupdate hooks for python3.13... 74s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 74s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 74s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 74s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 74s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 74s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 74s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 75s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 75s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 75s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 75s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 75s Preparing to unpack .../6-lto-disabled-list_71_all.deb ... 75s Unpacking lto-disabled-list (71) over (69) ... 75s Setting up lto-disabled-list (71) ... 75s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 75s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 75s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 75s Setting up apt (3.1.8ubuntu1) ... 75s Setting up python3 (3.13.7-2) ... 76s running python rtupdate hooks for python3.13... 76s running python post-rtupdate hooks for python3.13... 76s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 76s Processing triggers for man-db (2.13.1-1) ... 78s Processing triggers for libc-bin (2.42-0ubuntu3) ... 78s autopkgtest [22:27:21]: upgrading testbed (apt dist-upgrade and autopurge) 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s autopkgtest [22:27:24]: rebooting testbed after setup commands that affected boot 101s autopkgtest [22:27:44]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 103s autopkgtest [22:27:46]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 106s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (dsc) [2280 B] 106s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (tar) [1290 kB] 106s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (diff) [7464 B] 107s gpgv: Signature made Mon Feb 3 14:50:02 2025 UTC 107s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 107s gpgv: issuer "merkys@debian.org" 107s gpgv: Can't check signature: No public key 107s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: no acceptable signature found 107s autopkgtest [22:27:50]: testing package gemmi version 0.6.5+ds-3 107s autopkgtest [22:27:50]: build not needed 109s autopkgtest [22:27:52]: test command1: preparing testbed 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Solving dependencies... 110s The following NEW packages will be installed: 110s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 110s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 110s python3-pluggy python3-pytest tao-pegtl-dev 110s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 15.2 MB of archives. 110s After this operation, 61.4 MB of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 111s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 111s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 111s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 111s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 111s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 gemmi amd64 0.6.5+ds-3 [1303 kB] 111s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 tao-pegtl-dev all 3.2.7-1 [59.6 kB] 111s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 gemmi-dev amd64 0.6.5+ds-3 [1305 kB] 111s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gemmi amd64 0.6.5+ds-3 [2721 kB] 111s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 111s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 111s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 111s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 112s Fetched 15.2 MB in 1s (12.2 MB/s) 112s Selecting previously unselected package python3-numpy-dev:amd64. 112s (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 ... 78439 files and directories currently installed.) 112s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 112s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 112s Selecting previously unselected package libblas3:amd64. 112s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 112s Unpacking libblas3:amd64 (3.12.1-6build1) ... 112s Selecting previously unselected package libgfortran5:amd64. 112s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 112s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 112s Selecting previously unselected package liblapack3:amd64. 112s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 112s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 112s Selecting previously unselected package python3-numpy. 112s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 112s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 112s Selecting previously unselected package gemmi. 112s Preparing to unpack .../05-gemmi_0.6.5+ds-3_amd64.deb ... 112s Unpacking gemmi (0.6.5+ds-3) ... 112s Selecting previously unselected package tao-pegtl-dev. 112s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 112s Unpacking tao-pegtl-dev (3.2.7-1) ... 112s Selecting previously unselected package gemmi-dev. 112s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_amd64.deb ... 112s Unpacking gemmi-dev (0.6.5+ds-3) ... 112s Selecting previously unselected package python3-gemmi. 112s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_amd64.deb ... 112s Unpacking python3-gemmi (0.6.5+ds-3) ... 113s Selecting previously unselected package python3-iniconfig. 113s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 113s Unpacking python3-iniconfig (1.1.1-2) ... 113s Selecting previously unselected package python3-packaging. 113s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 113s Unpacking python3-packaging (25.0-1) ... 113s Selecting previously unselected package python3-pluggy. 113s Preparing to unpack .../11-python3-pluggy_1.5.0-1_all.deb ... 113s Unpacking python3-pluggy (1.5.0-1) ... 113s Selecting previously unselected package python3-pytest. 113s Preparing to unpack .../12-python3-pytest_8.3.5-2_all.deb ... 113s Unpacking python3-pytest (8.3.5-2) ... 113s Setting up python3-iniconfig (1.1.1-2) ... 113s Setting up python3-gemmi (0.6.5+ds-3) ... 113s Setting up libblas3:amd64 (3.12.1-6build1) ... 113s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 113s Setting up python3-packaging (25.0-1) ... 113s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 113s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 113s Setting up python3-pluggy (1.5.0-1) ... 113s Setting up gemmi (0.6.5+ds-3) ... 113s Setting up tao-pegtl-dev (3.2.7-1) ... 113s Setting up liblapack3:amd64 (3.12.1-6build1) ... 113s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 113s Setting up python3-pytest (8.3.5-2) ... 114s Setting up gemmi-dev (0.6.5+ds-3) ... 114s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 115s Processing triggers for man-db (2.13.1-1) ... 116s Processing triggers for libc-bin (2.42-0ubuntu3) ... 117s autopkgtest [22:28:00]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 117s autopkgtest [22:28:00]: test command1: [----------------------- 118s ........................................................................ [ 38%] 118s .............................s.................s..............ssssss.... [ 76%] 119s ............................................ [100%] 119s =========================== short test summary info ============================ 119s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 119s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 119s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 119s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 119s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 119s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 119s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 119s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 119s 180 passed, 8 skipped, 3 deselected in 0.81s 119s autopkgtest [22:28:02]: test command1: -----------------------] 119s autopkgtest [22:28:02]: test command1: - - - - - - - - - - results - - - - - - - - - - 119s command1 PASS 120s autopkgtest [22:28:03]: @@@@@@@@@@@@@@@@@@@@ summary 120s command1 PASS