0s autopkgtest [16:38:05]: starting date and time: 2024-11-14 16:38:05+0000 0s autopkgtest [16:38:05]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:38:05]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zdj9g4t0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade python-pdbfixer --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-6.secgroup --name adt-plucky-arm64-python-pdbfixer-20241114-163805-juju-7f2275-prod-proposed-migration-environment-15-a57a6448-fe05-4598-be83-0311b0996942 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 74s autopkgtest [16:39:19]: testbed dpkg architecture: arm64 75s autopkgtest [16:39:20]: testbed apt version: 2.9.8 75s autopkgtest [16:39:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [136 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [711 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [5488 B] 77s Fetched 2054 kB in 1s (1908 kB/s) 77s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Calculating upgrade... 80s The following packages will be upgraded: 80s libcap-ng0 pastebinit python3-systemd 80s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 76.6 kB of archives. 80s After this operation, 349 kB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 81s Fetched 76.6 kB in 0s (224 kB/s) 82s (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 ... 79925 files and directories currently installed.) 82s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 82s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 82s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 82s (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 ... 79925 files and directories currently installed.) 82s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 82s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 82s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 82s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 82s Setting up pastebinit (1.7.1-1) ... 82s Setting up python3-systemd (235-1build5) ... 82s Processing triggers for man-db (2.12.1-3) ... 83s Processing triggers for libc-bin (2.40-1ubuntu3) ... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 85s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 86s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [16:39:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 92s autopkgtest [16:39:37]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pdbfixer 94s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (dsc) [2166 B] 94s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (tar) [648 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (diff) [2980 B] 94s gpgv: Signature made Tue Jul 4 05:45:38 2023 UTC 94s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 94s gpgv: issuer "merkys@debian.org" 94s gpgv: Can't check signature: No public key 94s dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-3.dsc: no acceptable signature found 94s autopkgtest [16:39:39]: testing package python-pdbfixer version 1.9-3 94s autopkgtest [16:39:39]: build not needed 95s autopkgtest [16:39:40]: test command1: preparing testbed 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Starting pkgProblemResolver with broken count: 0 98s Starting 2 pkgProblemResolver with broken count: 0 98s Done 99s The following additional packages will be installed: 99s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 99s python3-iniconfig python3-numpy python3-openmm python3-packaging 99s python3-pdbfixer python3-pluggy python3-pytest 99s Suggested packages: 99s gcc gfortran python-numpy-doc python3-dev 99s The following NEW packages will be installed: 99s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 99s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 99s python3-packaging python3-pdbfixer python3-pluggy python3-pytest 99s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 16.5 MB/16.5 MB of archives. 99s After this operation, 127 MB of additional disk space will be used. 99s Get:1 /tmp/autopkgtest.VLm40R/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 99s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 100s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 100s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-1 [986 kB] 100s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-1 [333 kB] 100s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 100s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 100s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openmm arm64 8.1.2+dfsg-1 [7401 kB] 100s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 100s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pdbfixer all 1.9-3 [463 kB] 100s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 100s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 101s Fetched 16.5 MB in 1s (13.6 MB/s) 101s Selecting previously unselected package libblas3:arm64. 101s (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 ... 79930 files and directories currently installed.) 101s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 101s Unpacking libblas3:arm64 (3.12.0-3build2) ... 101s Selecting previously unselected package libgfortran5:arm64. 101s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 101s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 101s Selecting previously unselected package liblapack3:arm64. 101s Preparing to unpack .../02-liblapack3_3.12.0-3build2_arm64.deb ... 101s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 101s Selecting previously unselected package libopenmm8.1. 101s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_arm64.deb ... 101s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 101s Selecting previously unselected package libopenmm-dev. 101s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_arm64.deb ... 101s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 101s Selecting previously unselected package python3-iniconfig. 101s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 101s Unpacking python3-iniconfig (1.1.1-2) ... 101s Selecting previously unselected package python3-numpy. 101s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 101s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 101s Selecting previously unselected package python3-openmm. 101s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_arm64.deb ... 101s Unpacking python3-openmm (8.1.2+dfsg-1) ... 102s Selecting previously unselected package python3-packaging. 102s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 102s Unpacking python3-packaging (24.1-1) ... 102s Selecting previously unselected package python3-pdbfixer. 102s Preparing to unpack .../09-python3-pdbfixer_1.9-3_all.deb ... 102s Unpacking python3-pdbfixer (1.9-3) ... 102s Selecting previously unselected package python3-pluggy. 102s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 102s Unpacking python3-pluggy (1.5.0-1) ... 102s Selecting previously unselected package python3-pytest. 102s Preparing to unpack .../11-python3-pytest_8.3.3-1_all.deb ... 102s Unpacking python3-pytest (8.3.3-1) ... 102s Selecting previously unselected package autopkgtest-satdep. 102s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 102s Unpacking autopkgtest-satdep (0) ... 102s Setting up python3-iniconfig (1.1.1-2) ... 102s Setting up libblas3:arm64 (3.12.0-3build2) ... 102s 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 102s Setting up python3-packaging (24.1-1) ... 102s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 102s Setting up python3-pluggy (1.5.0-1) ... 103s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 103s Setting up liblapack3:arm64 (3.12.0-3build2) ... 103s 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 103s Setting up python3-pytest (8.3.3-1) ... 103s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 103s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 105s Setting up python3-openmm (8.1.2+dfsg-1) ... 105s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 105s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 105s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 105s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 105s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 105s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 105s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 105s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 105s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 105s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 105s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 105s "(?:\s*#.*$)" "|" # comments (dumped) 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 105s "(\S+)" # unquoted words 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 105s """ Tokenizer method for the mmCIF syntax file - 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 105s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 105s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 105s "(?:\s*#.*$)" "|" # comments (dumped) 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 105s "(\S+)" # unquoted words 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 105s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 105s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 105s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 105s "(?:\s*#.*$)" "|" # comments (dumped) 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 105s "(\S+)" # unquoted words 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 105s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 105s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 105s "(?:\s*#.*$)" "|" # comments (dumped) 105s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 105s "(\S+)" # unquoted words 105s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 105s pattern = re.compile('bias_(.*)_(.*)\.npy') 105s /usr/lib/python3/dist-packages/openmm/openmm.py:10429: SyntaxWarning: invalid escape sequence '\S' 105s match = re.search("<([^?]\S*)", inputString) 105s Setting up python3-pdbfixer (1.9-3) ... 106s Setting up autopkgtest-satdep (0) ... 106s Processing triggers for man-db (2.12.1-3) ... 106s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s (Reading database ... 81654 files and directories currently installed.) 110s Removing autopkgtest-satdep (0) ... 110s autopkgtest [16:39:55]: test command1: pytest-3 pdbfixer/tests/test_removechains.py 110s autopkgtest [16:39:55]: test command1: [----------------------- 111s ============================= test session starts ============================== 111s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 111s rootdir: /tmp/autopkgtest.VLm40R/build.mQI/src 111s plugins: typeguard-4.4.1 111s collected 2 items 111s 120s pdbfixer/tests/test_removechains.py .. [100%] 120s 120s =============================== warnings summary =============================== 120s pdbfixer/pdbfixer.py:58 120s /tmp/autopkgtest.VLm40R/build.mQI/src/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 120s from pkg_resources import resource_filename 120s 120s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 120s ========================= 2 passed, 1 warning in 9.41s ========================= 121s autopkgtest [16:40:06]: test command1: -----------------------] 121s autopkgtest [16:40:06]: test command1: - - - - - - - - - - results - - - - - - - - - - 121s command1 PASS 121s autopkgtest [16:40:06]: @@@@@@@@@@@@@@@@@@@@ summary 121s command1 PASS 134s nova [W] Skipping flock in bos03-arm64 134s Creating nova instance adt-plucky-arm64-python-pdbfixer-20241114-163805-juju-7f2275-prod-proposed-migration-environment-15-a57a6448-fe05-4598-be83-0311b0996942 from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...