0s autopkgtest [03:18:35]: starting date and time: 2024-06-08 03:18:35+0000 0s autopkgtest [03:18:35]: git checkout: 433ed4c Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [03:18:35]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._jvjyvm_/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.242 lxd-armhf-10.145.243.242:autopkgtest/ubuntu/oracular/armhf 22s autopkgtest [03:18:57]: testbed dpkg architecture: armhf 24s autopkgtest [03:18:59]: testbed apt version: 2.9.3 24s autopkgtest [03:18:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 31s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 32s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [331 kB] 32s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [1680 B] 32s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 32s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 32s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [35.4 kB] 32s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted armhf Packages [1860 B] 32s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [243 kB] 32s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1768 B] 32s Fetched 777 kB in 1s (1053 kB/s) 32s Reading package lists... 48s tee: /proc/self/fd/2: Permission denied 69s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 69s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 71s Reading package lists... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s 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... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [03:19:49]: rebooting testbed after setup commands that affected boot 113s autopkgtest [03:20:28]: testbed running kernel: Linux 6.5.0-35-generic #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 7 11:19:33 UTC 2 139s autopkgtest [03:20:54]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 158s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (dsc) [2280 B] 158s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (tar) [1290 kB] 158s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-1 (diff) [7104 B] 158s gpgv: Signature made Tue May 21 10:42:01 2024 UTC 158s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 158s gpgv: issuer "merkys@debian.org" 158s gpgv: Can't check signature: No public key 158s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-1.dsc: no acceptable signature found 158s autopkgtest [03:21:13]: testing package gemmi version 0.6.5+ds-1 160s autopkgtest [03:21:15]: build not needed 162s autopkgtest [03:21:17]: test command1: preparing testbed 172s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s The following additional packages will be installed: 175s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 175s python3-iniconfig python3-numpy python3-packaging python3-pluggy 175s python3-pytest 175s Suggested packages: 175s gcc gfortran python-numpy-doc python3-dev 175s The following NEW packages will be installed: 175s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 175s python3-gemmi python3-iniconfig python3-numpy python3-packaging 175s python3-pluggy python3-pytest 175s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 11.1 MB/11.1 MB of archives. 175s After this operation, 36.2 MB of additional disk space will be used. 175s Get:1 /tmp/autopkgtest.lhkchZ/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [732 B] 175s Get:2 http://ftpmaster.internal/ubuntu oracular/universe armhf gemmi armhf 0.6.5+ds-1 [1194 kB] 176s Get:3 http://ftpmaster.internal/ubuntu oracular/universe armhf gemmi-dev armhf 0.6.5+ds-1 [1211 kB] 176s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 176s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 176s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 176s Get:7 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-gemmi armhf 0.6.5+ds-1 [2316 kB] 176s Get:8 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 176s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 176s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.0-1 [41.1 kB] 176s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 176s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-pytest all 8.2.2-1ubuntu1 [250 kB] 177s Fetched 11.1 MB in 1s (11.7 MB/s) 177s Selecting previously unselected package gemmi. 177s (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 ... 58338 files and directories currently installed.) 177s Preparing to unpack .../00-gemmi_0.6.5+ds-1_armhf.deb ... 177s Unpacking gemmi (0.6.5+ds-1) ... 177s Selecting previously unselected package gemmi-dev. 177s Preparing to unpack .../01-gemmi-dev_0.6.5+ds-1_armhf.deb ... 177s Unpacking gemmi-dev (0.6.5+ds-1) ... 177s Selecting previously unselected package libblas3:armhf. 177s Preparing to unpack .../02-libblas3_3.12.0-3build1_armhf.deb ... 177s Unpacking libblas3:armhf (3.12.0-3build1) ... 177s Selecting previously unselected package libgfortran5:armhf. 177s Preparing to unpack .../03-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 177s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 177s Selecting previously unselected package liblapack3:armhf. 177s Preparing to unpack .../04-liblapack3_3.12.0-3build1_armhf.deb ... 177s Unpacking liblapack3:armhf (3.12.0-3build1) ... 177s Selecting previously unselected package python3-gemmi. 177s Preparing to unpack .../05-python3-gemmi_0.6.5+ds-1_armhf.deb ... 177s Unpacking python3-gemmi (0.6.5+ds-1) ... 177s Selecting previously unselected package python3-iniconfig. 177s Preparing to unpack .../06-python3-iniconfig_1.1.1-2_all.deb ... 177s Unpacking python3-iniconfig (1.1.1-2) ... 177s Selecting previously unselected package python3-numpy. 177s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 177s Unpacking python3-numpy (1:1.26.4+ds-10) ... 178s Selecting previously unselected package python3-packaging. 178s Preparing to unpack .../08-python3-packaging_24.0-1_all.deb ... 178s Unpacking python3-packaging (24.0-1) ... 178s Selecting previously unselected package python3-pluggy. 178s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 178s Unpacking python3-pluggy (1.5.0-1) ... 178s Selecting previously unselected package python3-pytest. 178s Preparing to unpack .../10-python3-pytest_8.2.2-1ubuntu1_all.deb ... 178s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 178s Selecting previously unselected package autopkgtest-satdep. 178s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 178s Unpacking autopkgtest-satdep (0) ... 178s Setting up python3-iniconfig (1.1.1-2) ... 178s Setting up python3-gemmi (0.6.5+ds-1) ... 178s Setting up gemmi-dev (0.6.5+ds-1) ... 178s Setting up libblas3:armhf (3.12.0-3build1) ... 178s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 178s Setting up python3-packaging (24.0-1) ... 178s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 178s Setting up python3-pluggy (1.5.0-1) ... 178s Setting up gemmi (0.6.5+ds-1) ... 178s Setting up liblapack3:armhf (3.12.0-3build1) ... 178s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 178s Setting up python3-pytest (8.2.2-1ubuntu1) ... 179s Setting up python3-numpy (1:1.26.4+ds-10) ... 181s Setting up autopkgtest-satdep (0) ... 181s Processing triggers for man-db (2.12.1-1) ... 182s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 196s (Reading database ... 59554 files and directories currently installed.) 196s Removing autopkgtest-satdep (0) ... 201s autopkgtest [03:21:56]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 201s autopkgtest [03:21:56]: test command1: [----------------------- 204s ........................................................................ [ 38%] 205s .............................s.................s..............ssssss.... [ 76%] 205s ............................................ [100%] 205s =========================== short test summary info ============================ 205s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 205s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 205s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 205s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 205s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 205s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 205s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 205s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 205s 180 passed, 8 skipped, 3 deselected in 1.41s 205s autopkgtest [03:22:00]: test command1: -----------------------] 209s autopkgtest [03:22:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 209s command1 PASS 213s autopkgtest [03:22:08]: @@@@@@@@@@@@@@@@@@@@ summary 213s command1 PASS