0s autopkgtest [08:58:57]: starting date and time: 2024-06-08 08:58:57+0000 0s autopkgtest [08:58:57]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [08:58:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r4jly6tr/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-2@bos03-arm64-30.secgroup --name adt-oracular-arm64-gemmi-20240608-085857-juju-7f2275-prod-proposed-migration-environment-2-d75791d0-e853-4f47-b2e9-d85928b76de4 --image adt/ubuntu-oracular-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 753s autopkgtest [09:11:30]: testbed dpkg architecture: arm64 753s autopkgtest [09:11:30]: testbed apt version: 2.9.3 753s autopkgtest [09:11:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 754s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 755s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [1680 B] 755s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 755s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.2 kB] 755s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [334 kB] 755s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [67.7 kB] 755s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [31.8 kB] 755s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [296 kB] 755s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [9192 B] 755s Fetched 903 kB in 2s (408 kB/s) 755s Reading package lists... 759s Reading package lists... 759s Building dependency tree... 759s Reading state information... 760s Calculating upgrade... 761s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 762s Reading package lists... 762s Building dependency tree... 762s Reading state information... 762s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 765s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 765s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 765s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 765s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 767s Reading package lists... 767s Reading package lists... 767s Building dependency tree... 767s Reading state information... 768s Calculating upgrade... 768s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 768s Reading package lists... 768s Building dependency tree... 768s Reading state information... 769s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 773s autopkgtest [09:11:50]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 773s autopkgtest [09:11:50]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 779s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (dsc) [2280 B] 779s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (tar) [1290 kB] 779s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (diff) [7104 B] 780s gpgv: Signature made Tue May 21 10:42:01 2024 UTC 780s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 780s gpgv: issuer "merkys@debian.org" 780s gpgv: Can't check signature: No public key 780s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-1.dsc: no acceptable signature found 781s autopkgtest [09:11:58]: testing package gemmi version 0.6.5+ds-1 781s autopkgtest [09:11:58]: build not needed 782s autopkgtest [09:11:59]: test command1: preparing testbed 783s Reading package lists... 783s Building dependency tree... 783s Reading state information... 784s Starting pkgProblemResolver with broken count: 0 784s Starting 2 pkgProblemResolver with broken count: 0 784s Done 784s The following additional packages will be installed: 784s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 784s python3-iniconfig python3-numpy python3-packaging python3-pluggy 784s python3-pytest 784s Suggested packages: 784s gcc gfortran python-numpy-doc python3-dev 785s The following NEW packages will be installed: 785s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 785s python3-gemmi python3-iniconfig python3-numpy python3-packaging 785s python3-pluggy python3-pytest 785s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 785s Need to get 11.1 MB/11.1 MB of archives. 785s After this operation, 44.4 MB of additional disk space will be used. 785s Get:1 /tmp/autopkgtest.1oSXtV/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [732 B] 788s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 gemmi arm64 0.6.5+ds-1 [1027 kB] 789s Get:3 http://ftpmaster.internal/ubuntu oracular/universe arm64 gemmi-dev arm64 0.6.5+ds-1 [1200 kB] 789s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 789s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 789s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 789s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-gemmi arm64 0.6.5+ds-1 [2144 kB] 789s Get:8 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 789s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 789s Get:10 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 789s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 789s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 790s Fetched 11.1 MB in 4s (2544 kB/s) 790s Selecting previously unselected package gemmi. 791s (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 ... 78200 files and directories currently installed.) 791s Preparing to unpack .../00-gemmi_0.6.5+ds-1_arm64.deb ... 791s Unpacking gemmi (0.6.5+ds-1) ... 791s Selecting previously unselected package gemmi-dev. 791s Preparing to unpack .../01-gemmi-dev_0.6.5+ds-1_arm64.deb ... 791s Unpacking gemmi-dev (0.6.5+ds-1) ... 791s Selecting previously unselected package libblas3:arm64. 791s Preparing to unpack .../02-libblas3_3.12.0-3build1_arm64.deb ... 791s Unpacking libblas3:arm64 (3.12.0-3build1) ... 791s Selecting previously unselected package libgfortran5:arm64. 791s Preparing to unpack .../03-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 791s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 791s Selecting previously unselected package liblapack3:arm64. 791s Preparing to unpack .../04-liblapack3_3.12.0-3build1_arm64.deb ... 791s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 791s Selecting previously unselected package python3-gemmi. 791s Preparing to unpack .../05-python3-gemmi_0.6.5+ds-1_arm64.deb ... 791s Unpacking python3-gemmi (0.6.5+ds-1) ... 791s Selecting previously unselected package python3-iniconfig. 791s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 791s Unpacking python3-iniconfig (1.1.1-2) ... 791s Selecting previously unselected package python3-numpy. 791s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 791s Unpacking python3-numpy (1:1.26.4+ds-10) ... 791s Selecting previously unselected package python3-packaging. 792s Preparing to unpack .../08-python3-packaging_24.0-1_all.deb ... 792s Unpacking python3-packaging (24.0-1) ... 792s Selecting previously unselected package python3-pluggy. 792s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 792s Unpacking python3-pluggy (1.5.0-1) ... 792s Selecting previously unselected package python3-pytest. 792s Preparing to unpack .../10-python3-pytest_8.2.2-1ubuntu1_all.deb ... 792s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 792s Selecting previously unselected package autopkgtest-satdep. 792s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 792s Unpacking autopkgtest-satdep (0) ... 792s Setting up python3-iniconfig (1.1.1-2) ... 792s Setting up python3-gemmi (0.6.5+ds-1) ... 792s Setting up gemmi-dev (0.6.5+ds-1) ... 792s Setting up libblas3:arm64 (3.12.0-3build1) ... 792s 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 792s Setting up python3-packaging (24.0-1) ... 792s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 792s Setting up python3-pluggy (1.5.0-1) ... 793s Setting up gemmi (0.6.5+ds-1) ... 793s Setting up liblapack3:arm64 (3.12.0-3build1) ... 793s 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 793s Setting up python3-pytest (8.2.2-1ubuntu1) ... 793s Setting up python3-numpy (1:1.26.4+ds-10) ... 795s Setting up autopkgtest-satdep (0) ... 795s Processing triggers for man-db (2.12.1-1) ... 796s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 801s (Reading database ... 79415 files and directories currently installed.) 801s Removing autopkgtest-satdep (0) ... 802s autopkgtest [09:12:19]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 802s autopkgtest [09:12:19]: test command1: [----------------------- 803s ........................................................................ [ 38%] 804s .............................s.................s..............ssssss.... [ 76%] 804s ............................................ [100%] 804s =========================== short test summary info ============================ 804s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 804s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 804s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 804s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 804s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 804s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 804s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 804s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 804s 180 passed, 8 skipped, 3 deselected in 1.55s 805s autopkgtest [09:12:22]: test command1: -----------------------] 806s command1 PASS 806s autopkgtest [09:12:23]: test command1: - - - - - - - - - - results - - - - - - - - - - 807s autopkgtest [09:12:24]: @@@@@@@@@@@@@@@@@@@@ summary 807s command1 PASS 867s nova [W] Skipping flock in bos03-arm64 867s Creating nova instance adt-oracular-arm64-gemmi-20240608-085857-juju-7f2275-prod-proposed-migration-environment-2-d75791d0-e853-4f47-b2e9-d85928b76de4 from image adt/ubuntu-oracular-arm64-server-20240608.img (UUID 22fa5d69-8269-442f-bb5d-fd1454f7b08f)...