0s autopkgtest [09:25:09]: starting date and time: 2025-01-17 09:25:09+0000 0s autopkgtest [09:25:09]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [09:25:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wt9pdl59/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade python-pdbfixer --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-12.secgroup --name adt-plucky-amd64-python-pdbfixer-20250117-092509-juju-7f2275-prod-proposed-migration-environment-2-7bd7c4b9-c447-4fd0-ae3e-63dc4f7530cd --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [09:25:58]: testbed dpkg architecture: amd64 49s autopkgtest [09:25:58]: testbed apt version: 2.9.18 50s autopkgtest [09:25:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [09:25:59]: testbed release detected to be: None 51s autopkgtest [09:26:00]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [171 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [886 kB] 52s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.0 kB] 52s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [223 kB] 52s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [327 kB] 52s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 52s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 52s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [461 kB] 52s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1080 kB] 52s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [7684 B] 52s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [27.1 kB] 52s Fetched 3326 kB in 1s (3286 kB/s) 53s Reading package lists... 53s + lsb_release --codename --short 53s + RELEASE=plucky 53s + cat 53s + [ plucky != trusty ] 53s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s libgudev-1.0-0 usb.ids 54s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 239 kB of archives. 54s After this operation, 0 B of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 usb.ids all 2025.01.14-1 [223 kB] 54s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgudev-1.0-0 amd64 1:238-6 [15.8 kB] 55s Fetched 239 kB in 0s (497 kB/s) 55s (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 ... 75824 files and directories currently installed.) 55s Preparing to unpack .../usb.ids_2025.01.14-1_all.deb ... 55s Unpacking usb.ids (2025.01.14-1) over (2024.12.04-1) ... 55s Preparing to unpack .../libgudev-1.0-0_1%3a238-6_amd64.deb ... 55s Unpacking libgudev-1.0-0:amd64 (1:238-6) over (1:238-5ubuntu1) ... 55s Setting up usb.ids (2025.01.14-1) ... 55s Setting up libgudev-1.0-0:amd64 (1:238-6) ... 55s Processing triggers for libc-bin (2.40-4ubuntu1) ... 55s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 55s + /usr/lib/apt/apt-helper analyze-pattern ?true 55s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 56s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 56s + grep -q trusty /etc/lsb-release 56s + [ ! -d /usr/share/doc/unattended-upgrades ] 56s + [ ! -d /usr/share/doc/lxd ] 56s + [ ! -d /usr/share/doc/lxd-client ] 56s + [ ! -d /usr/share/doc/snapd ] 56s + type iptables 56s + cat 56s + chmod 755 /etc/rc.local 56s + . /etc/rc.local 56s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 56s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 56s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 56s + uname -m 56s + [ x86_64 = ppc64le ] 56s + [ -d /run/systemd/system ] 56s + systemd-detect-virt --quiet --vm 56s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 56s + cat 56s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 56s + echo COMPRESS=lz4 56s + sync 56s autopkgtest [09:26:05]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 57s Starting 2 pkgProblemResolver with broken count: 0 57s Done 57s Entering ResolveByKeep 57s 57s The following packages were automatically installed and are no longer required: 57s python3.12 python3.12-minimal 57s Use 'sudo apt autoremove' to remove them. 57s The following NEW packages will be installed: 57s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 57s The following packages will be upgraded: 57s libpython3-stdlib python3 python3-minimal 58s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 6118 kB of archives. 58s After this operation, 22.7 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.1-2 [881 kB] 58s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.1-2 [2358 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.13.1-1~exp2 [27.6 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.13.1-1~exp2 [23.9 kB] 58s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [2088 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.1-2 [729 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.13.1-1~exp2 [10.2 kB] 59s Fetched 6118 kB in 1s (7866 kB/s) 59s Selecting previously unselected package libpython3.13-minimal:amd64. 59s (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 ... 75824 files and directories currently installed.) 59s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_amd64.deb ... 59s Unpacking libpython3.13-minimal:amd64 (3.13.1-2) ... 59s Selecting previously unselected package python3.13-minimal. 59s Preparing to unpack .../python3.13-minimal_3.13.1-2_amd64.deb ... 59s Unpacking python3.13-minimal (3.13.1-2) ... 59s Setting up libpython3.13-minimal:amd64 (3.13.1-2) ... 59s Setting up python3.13-minimal (3.13.1-2) ... 59s (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 ... 76144 files and directories currently installed.) 59s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_amd64.deb ... 59s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 59s Setting up python3-minimal (3.13.1-1~exp2) ... 60s (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 ... 76144 files and directories currently installed.) 60s Preparing to unpack .../python3_3.13.1-1~exp2_amd64.deb ... 60s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 60s Selecting previously unselected package libpython3.13-stdlib:amd64. 60s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_amd64.deb ... 60s Unpacking libpython3.13-stdlib:amd64 (3.13.1-2) ... 60s Selecting previously unselected package python3.13. 60s Preparing to unpack .../python3.13_3.13.1-2_amd64.deb ... 60s Unpacking python3.13 (3.13.1-2) ... 60s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_amd64.deb ... 60s Unpacking libpython3-stdlib:amd64 (3.13.1-1~exp2) over (3.12.8-1) ... 60s Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... 60s Setting up libpython3-stdlib:amd64 (3.13.1-1~exp2) ... 60s Setting up python3.13 (3.13.1-2) ... 61s Setting up python3 (3.13.1-1~exp2) ... 61s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 61s for fn in glob1(directory, "%s.*" % fname): 61s Processing triggers for man-db (2.13.0-1) ... 61s Processing triggers for systemd (257-2ubuntu1) ... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Starting pkgProblemResolver with broken count: 0 62s Starting 2 pkgProblemResolver with broken count: 0 62s Done 62s The following packages will be REMOVED: 62s python3.12* python3.12-minimal* 63s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 63s After this operation, 8926 kB disk space will be freed. 63s (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 ... 76561 files and directories currently installed.) 63s Removing python3.12 (3.12.8-3) ... 63s Removing python3.12-minimal (3.12.8-3) ... 63s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 63s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 63s Processing triggers for man-db (2.13.0-1) ... 64s Processing triggers for systemd (257-2ubuntu1) ... 64s (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 ... 76533 files and directories currently installed.) 64s Purging configuration files for python3.12-minimal (3.12.8-3) ... 67s autopkgtest [09:26:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 67s autopkgtest [09:26:16]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pdbfixer 68s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (dsc) [2196 B] 68s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (tar) [648 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (diff) [3032 B] 69s gpgv: Signature made Sat Nov 16 13:59:37 2024 UTC 69s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 69s gpgv: issuer "tchet@debian.org" 69s gpgv: Can't check signature: No public key 69s dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-4.dsc: no acceptable signature found 69s autopkgtest [09:26:18]: testing package python-pdbfixer version 1.9-4 69s autopkgtest [09:26:18]: build not needed 70s autopkgtest [09:26:19]: test command1: preparing testbed 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s The following NEW packages will be installed: 71s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 71s python3-iniconfig python3-legacy-cgi python3-numpy python3-openmm 71s python3-packaging python3-pdbfixer python3-pluggy python3-pytest 71s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 20.0 MB of archives. 71s After this operation, 148 MB of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 71s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-12ubuntu1 [909 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 72s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-2 [1123 kB] 72s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-2 [349 kB] 72s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 72s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-legacy-cgi all 2.6.1-2 [16.3 kB] 72s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [5319 kB] 72s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openmm amd64 8.1.2+dfsg-2 [7980 kB] 72s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 72s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pdbfixer all 1.9-4 [463 kB] 72s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 72s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 72s Fetched 20.0 MB in 1s (17.1 MB/s) 72s Selecting previously unselected package libblas3:amd64. 72s (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 ... 76533 files and directories currently installed.) 72s Preparing to unpack .../00-libblas3_3.12.0-4_amd64.deb ... 72s Unpacking libblas3:amd64 (3.12.0-4) ... 72s Selecting previously unselected package libgfortran5:amd64. 72s Preparing to unpack .../01-libgfortran5_14.2.0-12ubuntu1_amd64.deb ... 72s Unpacking libgfortran5:amd64 (14.2.0-12ubuntu1) ... 73s Selecting previously unselected package liblapack3:amd64. 73s Preparing to unpack .../02-liblapack3_3.12.0-4_amd64.deb ... 73s Unpacking liblapack3:amd64 (3.12.0-4) ... 73s Selecting previously unselected package libopenmm8.1. 73s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-2_amd64.deb ... 73s Unpacking libopenmm8.1 (8.1.2+dfsg-2) ... 73s Selecting previously unselected package libopenmm-dev. 73s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-2_amd64.deb ... 73s Unpacking libopenmm-dev (8.1.2+dfsg-2) ... 73s Selecting previously unselected package python3-iniconfig. 73s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 73s Unpacking python3-iniconfig (1.1.1-2) ... 73s Selecting previously unselected package python3-legacy-cgi. 73s Preparing to unpack .../06-python3-legacy-cgi_2.6.1-2_all.deb ... 73s Unpacking python3-legacy-cgi (2.6.1-2) ... 73s Selecting previously unselected package python3-numpy. 73s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-12_amd64.deb ... 73s Unpacking python3-numpy (1:1.26.4+ds-12) ... 73s Selecting previously unselected package python3-openmm. 73s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-2_amd64.deb ... 73s Unpacking python3-openmm (8.1.2+dfsg-2) ... 73s Selecting previously unselected package python3-packaging. 73s Preparing to unpack .../09-python3-packaging_24.2-1_all.deb ... 73s Unpacking python3-packaging (24.2-1) ... 73s Selecting previously unselected package python3-pdbfixer. 73s Preparing to unpack .../10-python3-pdbfixer_1.9-4_all.deb ... 73s Unpacking python3-pdbfixer (1.9-4) ... 73s Selecting previously unselected package python3-pluggy. 73s Preparing to unpack .../11-python3-pluggy_1.5.0-1_all.deb ... 73s Unpacking python3-pluggy (1.5.0-1) ... 73s Selecting previously unselected package python3-pytest. 73s Preparing to unpack .../12-python3-pytest_8.3.4-1_all.deb ... 73s Unpacking python3-pytest (8.3.4-1) ... 73s Setting up python3-iniconfig (1.1.1-2) ... 73s Setting up libblas3:amd64 (3.12.0-4) ... 74s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 74s Setting up python3-packaging (24.2-1) ... 74s Setting up libgfortran5:amd64 (14.2.0-12ubuntu1) ... 74s Setting up python3-pluggy (1.5.0-1) ... 74s Setting up python3-legacy-cgi (2.6.1-2) ... 74s Setting up libopenmm8.1 (8.1.2+dfsg-2) ... 74s Setting up liblapack3:amd64 (3.12.0-4) ... 74s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 74s Setting up python3-pytest (8.3.4-1) ... 74s Setting up libopenmm-dev (8.1.2+dfsg-2) ... 74s Setting up python3-numpy (1:1.26.4+ds-12) ... 75s Setting up python3-openmm (8.1.2+dfsg-2) ... 75s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 75s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 75s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 75s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 75s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 75s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 75s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 75s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 75s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 75s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 75s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 75s "(?:\s*#.*$)" "|" # comments (dumped) 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 75s "(\S+)" # unquoted words 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 75s """ Tokenizer method for the mmCIF syntax file - 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 75s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 75s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 75s "(?:\s*#.*$)" "|" # comments (dumped) 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 75s "(\S+)" # unquoted words 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 75s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 75s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 75s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 75s "(?:\s*#.*$)" "|" # comments (dumped) 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 75s "(\S+)" # unquoted words 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 75s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 75s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 75s "(?:\s*#.*$)" "|" # comments (dumped) 75s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 75s "(\S+)" # unquoted words 75s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 75s pattern = re.compile('bias_(.*)_(.*)\.npy') 76s /usr/lib/python3/dist-packages/openmm/openmm.py:19267: SyntaxWarning: invalid escape sequence '\S' 76s match = re.search("<([^?]\S*)", inputString) 76s Setting up python3-pdbfixer (1.9-4) ... 76s Processing triggers for man-db (2.13.0-1) ... 76s Processing triggers for libc-bin (2.40-4ubuntu1) ... 77s autopkgtest [09:26:26]: test command1: pytest-3 pdbfixer/tests/test_removechains.py 77s autopkgtest [09:26:26]: test command1: [----------------------- 78s ============================= test session starts ============================== 78s platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 78s rootdir: /tmp/autopkgtest.eWRdbc/build.Z5y/src 78s plugins: typeguard-4.4.1 78s collected 2 items 78s 82s pdbfixer/tests/test_removechains.py .. [100%] 82s 82s =============================== warnings summary =============================== 82s :488 82s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 82s 82s :488 82s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 82s 82s :488 82s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 82s 82s pdbfixer/pdbfixer.py:58 82s /tmp/autopkgtest.eWRdbc/build.Z5y/src/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 82s from pkg_resources import resource_filename 82s 82s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 82s ======================== 2 passed, 4 warnings in 5.07s ========================= 83s autopkgtest [09:26:32]: test command1: -----------------------] 83s autopkgtest [09:26:32]: test command1: - - - - - - - - - - results - - - - - - - - - - 83s command1 PASS 84s autopkgtest [09:26:33]: @@@@@@@@@@@@@@@@@@@@ summary 84s command1 PASS 101s nova [W] Skipping flock for amd64 101s Creating nova instance adt-plucky-amd64-python-pdbfixer-20250117-092509-juju-7f2275-prod-proposed-migration-environment-2-7bd7c4b9-c447-4fd0-ae3e-63dc4f7530cd from image adt/ubuntu-plucky-amd64-server-20250117.img (UUID 8f35863a-398a-4b7d-9594-544c7b7656c3)... 101s nova [W] Timed out waiting for 6b1c3a85-df43-4c5b-a6a3-dd600ba43213 to get deleted.