0s autopkgtest [20:11:45]: starting date and time: 2024-11-14 20:11:45+0000 0s autopkgtest [20:11:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:11:45]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ao3h2ro/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-3.secgroup --name adt-plucky-ppc64el-python-pdbfixer-20241114-201144-juju-7f2275-prod-proposed-migration-environment-15-8218c013-86d8-4716-8ac9-b93a5adfe491 --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/ 94s autopkgtest [20:13:19]: testbed dpkg architecture: ppc64el 94s autopkgtest [20:13:19]: testbed apt version: 2.9.8 94s autopkgtest [20:13:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 95s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [114 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [697 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B] 97s Fetched 1957 kB in 2s (1129 kB/s) 97s Reading package lists... 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 102s The following packages will be upgraded: 102s bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0 102s libjson-glib-1.0-common libnewt0.52 libutempter0 pastebinit python3-bpfcc 102s python3-newt python3-systemd whiptail 102s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 4678 kB of archives. 102s After this operation, 423 kB of additional disk space will be used. 102s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB] 104s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 104s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 104s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 104s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB] 104s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB] 104s Fetched 4678 kB in 2s (2175 kB/s) 104s (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.) 104s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ... 104s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ... 104s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ... 104s (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.) 104s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 104s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 104s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 105s (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.) 105s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ... 105s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 105s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ... 105s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 105s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ... 105s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 105s Preparing to unpack .../03-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ... 105s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 105s Preparing to unpack .../04-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ... 105s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 105s Preparing to unpack .../05-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ... 105s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ... 105s Preparing to unpack .../06-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ... 105s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ... 105s Preparing to unpack .../07-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 105s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 105s Preparing to unpack .../08-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 105s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 105s Preparing to unpack .../09-libutempter0_1.2.1-4_ppc64el.deb ... 105s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 105s Preparing to unpack .../10-pastebinit_1.7.1-1_all.deb ... 105s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 105s Preparing to unpack .../11-python3-systemd_235-1build5_ppc64el.deb ... 105s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 105s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ... 105s Setting up pastebinit (1.7.1-1) ... 105s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ... 106s Setting up libutempter0:ppc64el (1.2.1-4) ... 106s Setting up whiptail (0.52.24-2ubuntu4) ... 106s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 106s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ... 106s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ... 106s Setting up python3-systemd (235-1build5) ... 106s Setting up bpftrace (0.21.2-2ubuntu2) ... 106s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 106s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ... 106s Processing triggers for man-db (2.12.1-3) ... 107s Processing triggers for libc-bin (2.40-1ubuntu3) ... 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 108s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 110s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [20:13:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 114s autopkgtest [20:13:39]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pdbfixer 117s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (dsc) [2166 B] 117s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (tar) [648 kB] 117s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-3 (diff) [2980 B] 117s gpgv: Signature made Tue Jul 4 05:45:38 2023 UTC 117s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 117s gpgv: issuer "merkys@debian.org" 117s gpgv: Can't check signature: No public key 117s dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-3.dsc: no acceptable signature found 117s autopkgtest [20:13:42]: testing package python-pdbfixer version 1.9-3 117s autopkgtest [20:13:42]: build not needed 119s autopkgtest [20:13:44]: test command1: preparing testbed 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 124s The following additional packages will be installed: 124s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 124s python3-iniconfig python3-numpy python3-openmm python3-packaging 124s python3-pdbfixer python3-pluggy python3-pytest 124s Suggested packages: 124s gcc gfortran python-numpy-doc python3-dev 124s The following NEW packages will be installed: 124s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 124s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 124s python3-packaging python3-pdbfixer python3-pluggy python3-pytest 125s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 18.3 MB/18.3 MB of archives. 125s After this operation, 140 MB of additional disk space will be used. 125s Get:1 /tmp/autopkgtest.WEbbaX/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 125s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 125s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 126s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm8.1 ppc64el 8.1.2+dfsg-1 [922 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libopenmm-dev ppc64el 8.1.2+dfsg-1 [352 kB] 126s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 126s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 127s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openmm ppc64el 8.1.2+dfsg-1 [7509 kB] 128s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 128s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pdbfixer all 1.9-3 [463 kB] 128s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 128s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 128s Fetched 18.3 MB in 3s (5882 kB/s) 128s Selecting previously unselected package libblas3:ppc64el. 128s (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 ... 73773 files and directories currently installed.) 128s Preparing to unpack .../00-libblas3_3.12.0-3build2_ppc64el.deb ... 128s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 128s Selecting previously unselected package libgfortran5:ppc64el. 128s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 128s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 128s Selecting previously unselected package liblapack3:ppc64el. 128s Preparing to unpack .../02-liblapack3_3.12.0-3build2_ppc64el.deb ... 128s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 128s Selecting previously unselected package libopenmm8.1. 128s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_ppc64el.deb ... 128s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 128s Selecting previously unselected package libopenmm-dev. 128s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_ppc64el.deb ... 128s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 128s Selecting previously unselected package python3-iniconfig. 128s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 128s Unpacking python3-iniconfig (1.1.1-2) ... 128s Selecting previously unselected package python3-numpy. 128s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 128s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 129s Selecting previously unselected package python3-openmm. 129s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_ppc64el.deb ... 129s Unpacking python3-openmm (8.1.2+dfsg-1) ... 129s Selecting previously unselected package python3-packaging. 129s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 129s Unpacking python3-packaging (24.1-1) ... 129s Selecting previously unselected package python3-pdbfixer. 129s Preparing to unpack .../09-python3-pdbfixer_1.9-3_all.deb ... 129s Unpacking python3-pdbfixer (1.9-3) ... 129s Selecting previously unselected package python3-pluggy. 129s Preparing to unpack .../10-python3-pluggy_1.5.0-1_all.deb ... 129s Unpacking python3-pluggy (1.5.0-1) ... 129s Selecting previously unselected package python3-pytest. 129s Preparing to unpack .../11-python3-pytest_8.3.3-1_all.deb ... 129s Unpacking python3-pytest (8.3.3-1) ... 129s Selecting previously unselected package autopkgtest-satdep. 129s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 129s Unpacking autopkgtest-satdep (0) ... 129s Setting up python3-iniconfig (1.1.1-2) ... 129s Setting up libblas3:ppc64el (3.12.0-3build2) ... 129s 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 129s Setting up python3-packaging (24.1-1) ... 130s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 130s Setting up python3-pluggy (1.5.0-1) ... 130s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 130s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 130s 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 130s Setting up python3-pytest (8.3.3-1) ... 130s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 130s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 133s Setting up python3-openmm (8.1.2+dfsg-1) ... 133s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 133s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 133s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 133s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 133s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 133s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 133s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 133s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 133s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 133s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 133s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 133s "(?:\s*#.*$)" "|" # comments (dumped) 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 133s "(\S+)" # unquoted words 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 133s """ Tokenizer method for the mmCIF syntax file - 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 133s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 133s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 133s "(?:\s*#.*$)" "|" # comments (dumped) 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 133s "(\S+)" # unquoted words 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 133s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 133s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 133s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 133s "(?:\s*#.*$)" "|" # comments (dumped) 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 133s "(\S+)" # unquoted words 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 133s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 133s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 133s "(?:\s*#.*$)" "|" # comments (dumped) 133s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 133s "(\S+)" # unquoted words 133s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 133s pattern = re.compile('bias_(.*)_(.*)\.npy') 133s /usr/lib/python3/dist-packages/openmm/openmm.py:8376: SyntaxWarning: invalid escape sequence '\S' 133s match = re.search("<([^?]\S*)", inputString) 133s Setting up python3-pdbfixer (1.9-3) ... 134s Setting up autopkgtest-satdep (0) ... 134s Processing triggers for man-db (2.12.1-3) ... 134s Processing triggers for libc-bin (2.40-1ubuntu3) ... 137s (Reading database ... 75497 files and directories currently installed.) 137s Removing autopkgtest-satdep (0) ... 137s autopkgtest [20:14:02]: test command1: pytest-3 pdbfixer/tests/test_removechains.py 137s autopkgtest [20:14:02]: test command1: [----------------------- 138s ============================= test session starts ============================== 138s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 138s rootdir: /tmp/autopkgtest.WEbbaX/build.Fuk/src 138s plugins: typeguard-4.4.1 138s collected 2 items 138s 151s pdbfixer/tests/test_removechains.py .. [100%] 151s 151s =============================== warnings summary =============================== 151s pdbfixer/pdbfixer.py:58 151s /tmp/autopkgtest.WEbbaX/build.Fuk/src/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 151s from pkg_resources import resource_filename 151s 151s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 151s ======================== 2 passed, 1 warning in 13.05s ========================= 152s autopkgtest [20:14:17]: test command1: -----------------------] 152s autopkgtest [20:14:17]: test command1: - - - - - - - - - - results - - - - - - - - - - 152s command1 PASS 152s autopkgtest [20:14:17]: @@@@@@@@@@@@@@@@@@@@ summary 152s command1 PASS 157s nova [W] Using flock in prodstack6-ppc64el 157s Creating nova instance adt-plucky-ppc64el-python-pdbfixer-20241114-201144-juju-7f2275-prod-proposed-migration-environment-15-8218c013-86d8-4716-8ac9-b93a5adfe491 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...