2s autopkgtest [15:48:24]: starting date and time: 2024-08-07 15:48:24+0000 2s autopkgtest [15:48:24]: git checkout: 0328c1ca Merge branch 'dep-drop-broken-debugging' into 'master' 2s autopkgtest [15:48:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xx3xzew1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy,src:sphinx --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11build1 sphinx/7.4.7-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-40.secgroup --name adt-oracular-ppc64el-gemmi-20240807-154822-juju-7f2275-prod-proposed-migration-environment-2-4dd8ae47-09f7-41a2-bb57-0981aacc8568 --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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/ 68s autopkgtest [15:49:30]: testbed dpkg architecture: ppc64el 68s autopkgtest [15:49:30]: testbed apt version: 2.9.7 68s autopkgtest [15:49:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 70s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 70s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [8756 B] 70s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [80.8 kB] 70s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [624 kB] 70s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [10.1 kB] 70s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [140 kB] 70s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [3576 B] 70s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [2272 B] 70s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 70s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [718 kB] 70s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [21.3 kB] 70s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [4752 B] 70s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [388 B] 74s Fetched 1740 kB in 1s (1935 kB/s) 74s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s 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 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [15:49:46]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 84s autopkgtest [15:49:46]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 88s Get:1 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-2 (dsc) [2280 B] 88s Get:2 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-2 (tar) [1290 kB] 88s Get:3 http://ftpmaster.internal/ubuntu oracular/universe gemmi 0.6.5+ds-2 (diff) [7124 B] 88s gpgv: Signature made Tue Jul 9 09:03:26 2024 UTC 88s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 88s gpgv: issuer "merkys@debian.org" 88s gpgv: Can't check signature: No public key 88s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-2.dsc: no acceptable signature found 88s autopkgtest [15:49:50]: testing package gemmi version 0.6.5+ds-2 88s autopkgtest [15:49:50]: build not needed 89s autopkgtest [15:49:51]: test command1: preparing testbed 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Starting pkgProblemResolver with broken count: 0 91s Starting 2 pkgProblemResolver with broken count: 0 91s Done 91s The following additional packages will be installed: 91s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 91s python3-iniconfig python3-numpy python3-packaging python3-pluggy 91s python3-pytest tao-pegtl-dev 91s Suggested packages: 91s gcc gfortran python-numpy-doc python3-dev 91s The following NEW packages will be installed: 91s autopkgtest-satdep gemmi gemmi-dev libblas3 libgfortran5 liblapack3 91s python3-gemmi python3-iniconfig python3-numpy python3-packaging 91s python3-pluggy python3-pytest tao-pegtl-dev 91s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 13.7 MB/13.7 MB of archives. 91s After this operation, 55.8 MB of additional disk space will be used. 91s Get:1 /tmp/autopkgtest.IAldwV/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 91s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ppc64el gemmi ppc64el 0.6.5+ds-2 [1332 kB] 92s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ppc64el tao-pegtl-dev all 3.2.7-1 [59.6 kB] 92s Get:4 http://ftpmaster.internal/ubuntu oracular/universe ppc64el gemmi-dev ppc64el 0.6.5+ds-2 [1331 kB] 92s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 92s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.2.0-1ubuntu1 [571 kB] 92s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 92s Get:8 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-gemmi ppc64el 0.6.5+ds-2 [2548 kB] 93s Get:9 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 93s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 93s Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 93s Get:12 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 93s Get:13 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 93s Fetched 13.7 MB in 2s (9057 kB/s) 93s Selecting previously unselected package gemmi. 93s (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 ... 72527 files and directories currently installed.) 93s Preparing to unpack .../00-gemmi_0.6.5+ds-2_ppc64el.deb ... 93s Unpacking gemmi (0.6.5+ds-2) ... 93s Selecting previously unselected package tao-pegtl-dev. 93s Preparing to unpack .../01-tao-pegtl-dev_3.2.7-1_all.deb ... 93s Unpacking tao-pegtl-dev (3.2.7-1) ... 93s Selecting previously unselected package gemmi-dev. 93s Preparing to unpack .../02-gemmi-dev_0.6.5+ds-2_ppc64el.deb ... 93s Unpacking gemmi-dev (0.6.5+ds-2) ... 94s Selecting previously unselected package libblas3:ppc64el. 94s Preparing to unpack .../03-libblas3_3.12.0-3build1_ppc64el.deb ... 94s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 94s Selecting previously unselected package libgfortran5:ppc64el. 94s Preparing to unpack .../04-libgfortran5_14.2.0-1ubuntu1_ppc64el.deb ... 94s Unpacking libgfortran5:ppc64el (14.2.0-1ubuntu1) ... 94s Selecting previously unselected package liblapack3:ppc64el. 94s Preparing to unpack .../05-liblapack3_3.12.0-3build1_ppc64el.deb ... 94s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 94s Selecting previously unselected package python3-gemmi. 94s Preparing to unpack .../06-python3-gemmi_0.6.5+ds-2_ppc64el.deb ... 94s Unpacking python3-gemmi (0.6.5+ds-2) ... 94s Selecting previously unselected package python3-iniconfig. 94s Preparing to unpack .../07-python3-iniconfig_1.1.1-2_all.deb ... 94s Unpacking python3-iniconfig (1.1.1-2) ... 94s Selecting previously unselected package python3-numpy. 94s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 94s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 94s Selecting previously unselected package python3-packaging. 94s Preparing to unpack .../09-python3-packaging_24.1-1_all.deb ... 94s Unpacking python3-packaging (24.1-1) ... 94s Selecting previously unselected package python3-pluggy. 94s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 94s Unpacking python3-pluggy (1.5.0-1) ... 94s Selecting previously unselected package python3-pytest. 94s Preparing to unpack .../11-python3-pytest_7.4.4-1_all.deb ... 94s Unpacking python3-pytest (7.4.4-1) ... 94s Selecting previously unselected package autopkgtest-satdep. 94s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 94s Unpacking autopkgtest-satdep (0) ... 94s Setting up python3-iniconfig (1.1.1-2) ... 94s Setting up python3-gemmi (0.6.5+ds-2) ... 94s Setting up libblas3:ppc64el (3.12.0-3build1) ... 94s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 94s Setting up python3-packaging (24.1-1) ... 94s Setting up libgfortran5:ppc64el (14.2.0-1ubuntu1) ... 94s Setting up python3-pluggy (1.5.0-1) ... 94s Setting up gemmi (0.6.5+ds-2) ... 94s Setting up tao-pegtl-dev (3.2.7-1) ... 94s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 94s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 94s Setting up python3-pytest (7.4.4-1) ... 95s Setting up gemmi-dev (0.6.5+ds-2) ... 95s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 97s Setting up autopkgtest-satdep (0) ... 97s Processing triggers for man-db (2.12.1-2) ... 98s Processing triggers for libc-bin (2.39-0ubuntu9) ... 102s (Reading database ... 73945 files and directories currently installed.) 102s Removing autopkgtest-satdep (0) ... 103s autopkgtest [15:50:05]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 103s autopkgtest [15:50:05]: test command1: [----------------------- 104s ........................................................................ [ 38%] 104s .............................s.................s..............ssssss.... [ 76%] 104s ............................................ [100%] 104s =========================== short test summary info ============================ 104s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 104s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 104s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 104s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 104s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 104s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 104s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 104s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 104s 180 passed, 8 skipped, 3 deselected in 1.09s 105s autopkgtest [15:50:07]: test command1: -----------------------] 105s autopkgtest [15:50:07]: test command1: - - - - - - - - - - results - - - - - - - - - - 105s command1 PASS 106s autopkgtest [15:50:08]: @@@@@@@@@@@@@@@@@@@@ summary 106s command1 PASS 127s Creating nova instance adt-oracular-ppc64el-gemmi-20240807-154822-juju-7f2275-prod-proposed-migration-environment-2-4dd8ae47-09f7-41a2-bb57-0981aacc8568 from image adt/ubuntu-oracular-ppc64el-server-20240807.img (UUID 22d2510d-6872-4fc2-b88c-14c7e1eb3604)...