0s autopkgtest [23:00:58]: starting date and time: 2024-11-13 23:00:58+0000 0s autopkgtest [23:00:58]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [23:00:58]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n20qf0y_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-pdbfixer --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-16.secgroup --name adt-plucky-ppc64el-python-pdbfixer-20241113-230058-juju-7f2275-prod-proposed-migration-environment-15-7f1b9575-5e6a-461b-92e3-c2e49c823e7f --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 124s autopkgtest [23:03:02]: testbed dpkg architecture: ppc64el 124s autopkgtest [23:03:02]: testbed apt version: 2.9.8 124s autopkgtest [23:03:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 125s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 125s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 126s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB] 126s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [692 kB] 126s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 126s Fetched 1993 kB in 1s (2107 kB/s) 126s Reading package lists... 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 129s The following NEW packages will be installed: 129s python3.13-gdbm 129s The following packages will be upgraded: 129s bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0 129s libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3 129s python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail 129s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 129s Need to get 4700 kB of archives. 129s After this operation, 215 kB of additional disk space will be used. 129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 129s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 129s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 129s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 129s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 129s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 129s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 129s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 129s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 129s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 129s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 129s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 129s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 129s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 129s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 130s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 130s Fetched 4700 kB in 1s (6517 kB/s) 130s (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 ... 73767 files and directories currently installed.) 130s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 130s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 130s Setting up python3-minimal (3.12.7-1) ... 130s (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 ... 73767 files and directories currently installed.) 130s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 130s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 130s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 130s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 130s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 130s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 130s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 130s (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 ... 73767 files and directories currently installed.) 130s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 130s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 130s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 130s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 130s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 130s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 130s Selecting previously unselected package python3.13-gdbm. 130s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ... 130s Unpacking python3.13-gdbm (3.13.0-2) ... 130s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ... 130s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 130s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 130s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 131s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 131s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 131s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 131s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 131s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 131s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 131s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 131s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 131s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 131s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 131s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ... 131s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 131s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 131s Setting up libutempter0:ppc64el (1.2.1-4) ... 131s Setting up whiptail (0.52.24-2ubuntu4) ... 131s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 131s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 131s Setting up python3.13-gdbm (3.13.0-2) ... 131s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 131s Setting up bpftrace (0.21.2-2ubuntu2) ... 131s Setting up python3 (3.12.7-1) ... 131s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 131s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 131s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 131s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 131s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 131s Processing triggers for man-db (2.12.1-3) ... 132s Processing triggers for libc-bin (2.40-1ubuntu3) ... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu plucky-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... 135s Building dependency tree... 135s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s autopkgtest [23:03:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 138s autopkgtest [23:03:16]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pdbfixer 140s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (dsc) [2166 B] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (tar) [648 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (diff) [2980 B] 140s gpgv: Signature made Tue Jul 4 05:45:38 2023 UTC 140s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 140s gpgv: issuer "merkys@debian.org" 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-3.dsc: no acceptable signature found 140s autopkgtest [23:03:18]: testing package python-pdbfixer version 1.9-3 140s autopkgtest [23:03:18]: build not needed 142s autopkgtest [23:03:20]: test command1: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 146s The following additional packages will be installed: 146s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 146s python3-iniconfig python3-numpy python3-openmm python3-packaging 146s python3-pdbfixer python3-pluggy python3-pytest 146s Suggested packages: 146s gcc gfortran python-numpy-doc python3-dev 146s The following NEW packages will be installed: 146s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 146s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 146s python3-packaging python3-pdbfixer python3-pluggy python3-pytest 146s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 17.6 MB/17.6 MB of archives. 146s After this operation, 128 MB of additional disk space will be used. 146s Get:1 /tmp/autopkgtest.q76myM/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 146s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 146s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm8.1 ppc64el 8.1.2+dfsg-1 [922 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm-dev ppc64el 8.1.2+dfsg-1 [352 kB] 146s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 146s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 147s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openmm ppc64el 8.1.2+dfsg-1 [7509 kB] 147s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 147s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pdbfixer all 1.9-3 [463 kB] 147s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 147s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 147s Fetched 17.6 MB in 1s (14.3 MB/s) 147s Selecting previously unselected package libblas3:ppc64el. 147s (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 ... 73775 files and directories currently installed.) 147s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 147s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 147s Selecting previously unselected package libgfortran5:ppc64el. 147s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 147s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 147s Selecting previously unselected package liblapack3:ppc64el. 147s Preparing to unpack .../02-liblapack3_3.12.0-3build2_ppc64el.deb ... 147s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 147s Selecting previously unselected package libopenmm8.1. 147s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_ppc64el.deb ... 147s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 147s Selecting previously unselected package libopenmm-dev. 147s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_ppc64el.deb ... 147s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 147s Selecting previously unselected package python3-iniconfig. 147s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 147s Unpacking python3-iniconfig (1.1.1-2) ... 147s Selecting previously unselected package python3-numpy. 147s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 147s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 148s Selecting previously unselected package python3-openmm. 148s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_ppc64el.deb ... 148s Unpacking python3-openmm (8.1.2+dfsg-1) ... 148s Selecting previously unselected package python3-packaging. 148s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 148s Unpacking python3-packaging (24.1-1) ... 148s Selecting previously unselected package python3-pdbfixer. 148s Preparing to unpack .../09-python3-pdbfixer_1.9-3_all.deb ... 148s Unpacking python3-pdbfixer (1.9-3) ... 148s Selecting previously unselected package python3-pluggy. 148s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 148s Unpacking python3-pluggy (1.5.0-1) ... 148s Selecting previously unselected package python3-pytest. 148s Preparing to unpack .../11-python3-pytest_8.3.3-1_all.deb ... 148s Unpacking python3-pytest (8.3.3-1) ... 148s Selecting previously unselected package autopkgtest-satdep. 148s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 148s Unpacking autopkgtest-satdep (0) ... 148s Setting up python3-iniconfig (1.1.1-2) ... 148s Setting up libblas3:ppc64el (3.12.0-3build2) ... 148s 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 148s Setting up python3-packaging (24.1-1) ... 148s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 148s Setting up python3-pluggy (1.5.0-1) ... 148s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 148s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 148s 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 148s Setting up python3-pytest (8.3.3-1) ... 149s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 149s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 151s Setting up python3-openmm (8.1.2+dfsg-1) ... 151s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 151s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 151s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 151s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 151s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 151s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 151s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 151s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 151s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 151s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 151s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 151s "(?:\s*#.*$)" "|" # comments (dumped) 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 151s "(\S+)" # unquoted words 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 151s """ Tokenizer method for the mmCIF syntax file - 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 151s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 151s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 151s "(?:\s*#.*$)" "|" # comments (dumped) 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 151s "(\S+)" # unquoted words 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 151s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 151s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 151s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 151s "(?:\s*#.*$)" "|" # comments (dumped) 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 151s "(\S+)" # unquoted words 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 151s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 151s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 151s "(?:\s*#.*$)" "|" # comments (dumped) 151s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 151s "(\S+)" # unquoted words 151s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 151s pattern = re.compile('bias_(.*)_(.*)\.npy') 151s /usr/lib/python3/dist-packages/openmm/openmm.py:8376: SyntaxWarning: invalid escape sequence '\S' 151s match = re.search("<([^?]\S*)", inputString) 151s Setting up python3-pdbfixer (1.9-3) ... 151s Setting up autopkgtest-satdep (0) ... 151s Processing triggers for man-db (2.12.1-3) ... 152s Processing triggers for libc-bin (2.40-1ubuntu3) ... 154s (Reading database ... 75479 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [23:03:32]: test command1: pytest-3 pdbfixer/tests/test_removechains.py 154s autopkgtest [23:03:32]: test command1: [----------------------- 155s ============================= test session starts ============================== 155s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 155s rootdir: /tmp/autopkgtest.q76myM/build.w2N/src 155s plugins: typeguard-4.4.1 155s collected 2 items 155s 165s pdbfixer/tests/test_removechains.py .. [100%] 165s 165s =============================== warnings summary =============================== 165s pdbfixer/pdbfixer.py:58 165s /tmp/autopkgtest.q76myM/build.w2N/src/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 165s from pkg_resources import resource_filename 165s 165s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 165s ======================== 2 passed, 1 warning in 10.53s ========================= 166s autopkgtest [23:03:44]: test command1: -----------------------] 166s command1 PASS 166s autopkgtest [23:03:44]: test command1: - - - - - - - - - - results - - - - - - - - - - 166s autopkgtest [23:03:44]: @@@@@@@@@@@@@@@@@@@@ summary 166s command1 PASS 170s nova [W] Using flock in prodstack6-ppc64el 170s Creating nova instance adt-plucky-ppc64el-python-pdbfixer-20241113-230058-juju-7f2275-prod-proposed-migration-environment-15-7f1b9575-5e6a-461b-92e3-c2e49c823e7f from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...