4s autopkgtest [00:19:36]: starting date and time: 2024-06-08 00:19:36+0000 5s autopkgtest [00:19:37]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 5s autopkgtest [00:19:37]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2olyx_df/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-103.secgroup --name adt-oracular-amd64-gemmi-20240608-001927-juju-7f2275-prod-proposed-migration-environment-3-c3971cf9-6c8c-4763-9a5c-f30253bf97ab --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 128s autopkgtest [00:21:40]: testbed dpkg architecture: amd64 128s autopkgtest [00:21:40]: testbed apt version: 2.9.3 128s autopkgtest [00:21:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 129s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 129s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 129s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 129s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 129s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 129s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 129s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 129s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 129s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 129s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 129s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 129s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 129s Fetched 1081 kB in 0s (4146 kB/s) 129s Reading package lists... 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 132s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [00:21:49]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 137s autopkgtest [00:21:49]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 138s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (dsc) [2280 B] 138s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (tar) [1290 kB] 138s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (diff) [7104 B] 139s gpgv: Signature made Tue May 21 10:42:01 2024 UTC 139s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 139s gpgv: issuer "merkys@debian.org" 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-1.dsc: no acceptable signature found 139s autopkgtest [00:21:51]: testing package gemmi version 0.6.5+ds-1 139s autopkgtest [00:21:51]: build not needed 139s autopkgtest [00:21:51]: test command1: preparing testbed 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s The following additional packages will be installed: 141s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 141s python3-iniconfig python3-numpy python3-packaging python3-pluggy 141s python3-pytest 141s Suggested packages: 141s gcc gfortran python-numpy-doc python3-dev 141s The following NEW packages will be installed: 141s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 141s python3-gemmi python3-iniconfig python3-numpy python3-packaging 141s python3-pluggy python3-pytest 141s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 13.4 MB/13.4 MB of archives. 141s After this operation, 53.9 MB of additional disk space will be used. 141s Get:1 /tmp/autopkgtest.8wKxPR/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [732 B] 141s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 gemmi amd64 0.6.5+ds-1 [1154 kB] 141s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 gemmi-dev amd64 0.6.5+ds-1 [1231 kB] 141s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 141s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 141s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 141s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-gemmi amd64 0.6.5+ds-1 [2461 kB] 141s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 141s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 141s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 141s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 141s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 142s Fetched 13.4 MB in 0s (48.9 MB/s) 142s Selecting previously unselected package gemmi. 142s (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 ... 74365 files and directories currently installed.) 142s Preparing to unpack .../00-gemmi_0.6.5+ds-1_amd64.deb ... 142s Unpacking gemmi (0.6.5+ds-1) ... 142s Selecting previously unselected package gemmi-dev. 142s Preparing to unpack .../01-gemmi-dev_0.6.5+ds-1_amd64.deb ... 142s Unpacking gemmi-dev (0.6.5+ds-1) ... 142s Selecting previously unselected package libblas3:amd64. 142s Preparing to unpack .../02-libblas3_3.12.0-3build1_amd64.deb ... 142s Unpacking libblas3:amd64 (3.12.0-3build1) ... 142s Selecting previously unselected package libgfortran5:amd64. 142s Preparing to unpack .../03-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 142s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 142s Selecting previously unselected package liblapack3:amd64. 142s Preparing to unpack .../04-liblapack3_3.12.0-3build1_amd64.deb ... 142s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 142s Selecting previously unselected package python3-gemmi. 142s Preparing to unpack .../05-python3-gemmi_0.6.5+ds-1_amd64.deb ... 142s Unpacking python3-gemmi (0.6.5+ds-1) ... 142s Selecting previously unselected package python3-iniconfig. 142s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 142s Unpacking python3-iniconfig (1.1.1-2) ... 142s Selecting previously unselected package python3-numpy. 143s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 143s Unpacking python3-numpy (1:1.26.4+ds-10) ... 143s Selecting previously unselected package python3-packaging. 143s Preparing to unpack .../08-python3-packaging_24.0-1_all.deb ... 143s Unpacking python3-packaging (24.0-1) ... 143s Selecting previously unselected package python3-pluggy. 143s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 143s Unpacking python3-pluggy (1.5.0-1) ... 143s Selecting previously unselected package python3-pytest. 143s Preparing to unpack .../10-python3-pytest_8.2.2-1ubuntu1_all.deb ... 143s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 143s Selecting previously unselected package autopkgtest-satdep. 143s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 143s Unpacking autopkgtest-satdep (0) ... 143s Setting up python3-iniconfig (1.1.1-2) ... 143s Setting up python3-gemmi (0.6.5+ds-1) ... 143s Setting up gemmi-dev (0.6.5+ds-1) ... 143s Setting up libblas3:amd64 (3.12.0-3build1) ... 143s 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 143s Setting up python3-packaging (24.0-1) ... 143s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 143s Setting up python3-pluggy (1.5.0-1) ... 143s Setting up gemmi (0.6.5+ds-1) ... 143s Setting up liblapack3:amd64 (3.12.0-3build1) ... 143s 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 143s Setting up python3-pytest (8.2.2-1ubuntu1) ... 144s Setting up python3-numpy (1:1.26.4+ds-10) ... 146s Setting up autopkgtest-satdep (0) ... 146s Processing triggers for man-db (2.12.1-1) ... 146s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 149s (Reading database ... 75580 files and directories currently installed.) 149s Removing autopkgtest-satdep (0) ... 150s autopkgtest [00:22:02]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 150s autopkgtest [00:22:02]: test command1: [----------------------- 151s ........................................................................ [ 38%] 151s .............................s.................s..............ssssss.... [ 76%] 151s ............................................ [100%] 151s =========================== short test summary info ============================ 151s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 151s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 151s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 151s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 151s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 151s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 151s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 151s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 151s 180 passed, 8 skipped, 3 deselected in 1.09s 151s autopkgtest [00:22:03]: test command1: -----------------------] 152s command1 PASS 152s autopkgtest [00:22:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 152s autopkgtest [00:22:04]: @@@@@@@@@@@@@@@@@@@@ summary 152s command1 PASS 164s nova [W] Skipping flock for amd64 164s Creating nova instance adt-oracular-amd64-gemmi-20240608-001927-juju-7f2275-prod-proposed-migration-environment-3-c3971cf9-6c8c-4763-9a5c-f30253bf97ab from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)...