0s autopkgtest [19:08:59]: starting date and time: 2025-01-03 19:08:59+0000 0s autopkgtest [19:08:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:08:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.07hlj6td/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-34.secgroup --name adt-plucky-arm64-python-pdbfixer-20250103-190859-juju-7f2275-prod-proposed-migration-environment-2-2e9c7f1b-eecd-432a-850d-7491ea7fb1a2 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 135s autopkgtest [19:11:14]: testbed dpkg architecture: arm64 135s autopkgtest [19:11:14]: testbed apt version: 2.9.18 136s autopkgtest [19:11:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 136s autopkgtest [19:11:15]: testbed release detected to be: None 137s autopkgtest [19:11:16]: updating testbed package index (apt update) 137s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 137s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 137s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 137s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 137s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 137s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.5 kB] 137s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [777 kB] 138s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 138s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [99.9 kB] 138s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 138s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [840 kB] 138s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [12.2 kB] 138s Fetched 1955 kB in 1s (1979 kB/s) 139s Reading package lists... 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 141s The following packages will be upgraded: 141s base-passwd bash-completion binutils binutils-aarch64-linux-gnu 141s binutils-common libbinutils libctf-nobfd0 libctf0 libgprofng0 libsframe1 141s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 5715 kB of archives. 141s After this operation, 143 kB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 base-passwd arm64 3.6.6 [53.6 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 bash-completion all 1:2.16.0-1 [214 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgprofng0 arm64 2.43.50.20241230-1ubuntu1 [781 kB] 141s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libctf0 arm64 2.43.50.20241230-1ubuntu1 [99.0 kB] 141s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libctf-nobfd0 arm64 2.43.50.20241230-1ubuntu1 [102 kB] 141s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils-aarch64-linux-gnu arm64 2.43.50.20241230-1ubuntu1 [3421 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libbinutils arm64 2.43.50.20241230-1ubuntu1 [782 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils arm64 2.43.50.20241230-1ubuntu1 [3254 B] 142s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 binutils-common arm64 2.43.50.20241230-1ubuntu1 [245 kB] 142s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libsframe1 arm64 2.43.50.20241230-1ubuntu1 [14.3 kB] 143s Preconfiguring packages ... 143s Fetched 5715 kB in 2s (3506 kB/s) 143s (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 ... 80060 files and directories currently installed.) 143s Preparing to unpack .../base-passwd_3.6.6_arm64.deb ... 143s Unpacking base-passwd (3.6.6) over (3.6.5) ... 143s Setting up base-passwd (3.6.6) ... 143s (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 ... 80060 files and directories currently installed.) 143s Preparing to unpack .../0-bash-completion_1%3a2.16.0-1_all.deb ... 143s Unpacking bash-completion (1:2.16.0-1) over (1:2.14.0-2) ... 144s Preparing to unpack .../1-libgprofng0_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking libgprofng0:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../2-libctf0_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking libctf0:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../3-libctf-nobfd0_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking libctf-nobfd0:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../4-binutils-aarch64-linux-gnu_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking binutils-aarch64-linux-gnu (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../5-libbinutils_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking libbinutils:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../6-binutils_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking binutils (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../7-binutils-common_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking binutils-common:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Preparing to unpack .../8-libsframe1_2.43.50.20241230-1ubuntu1_arm64.deb ... 144s Unpacking libsframe1:arm64 (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 144s Setting up binutils-common:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up libctf-nobfd0:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up libsframe1:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up bash-completion (1:2.16.0-1) ... 144s Setting up libbinutils:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up libctf0:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up libgprofng0:arm64 (2.43.50.20241230-1ubuntu1) ... 144s Setting up binutils-aarch64-linux-gnu (2.43.50.20241230-1ubuntu1) ... 144s Setting up binutils (2.43.50.20241230-1ubuntu1) ... 144s Processing triggers for libc-bin (2.40-4ubuntu1) ... 144s Processing triggers for man-db (2.13.0-1) ... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 147s autopkgtest [19:11:26]: upgrading testbed (apt dist-upgrade and autopurge) 147s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 150s Entering ResolveByKeep 150s 150s The following packages were automatically installed and are no longer required: 150s python3.12 python3.12-minimal 150s Use 'sudo apt autoremove' to remove them. 150s The following NEW packages will be installed: 150s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 150s The following packages will be upgraded: 150s libpython3-stdlib python3 python3-minimal 151s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 5992 kB of archives. 151s After this operation, 24.3 MB of additional disk space will be used. 151s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.13.1-1~exp2 [27.6 kB] 151s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.13.1-1~exp2 [23.9 kB] 151s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 152s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 152s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.13.1-1~exp2 [10.2 kB] 152s Fetched 5992 kB in 1s (4636 kB/s) 152s Selecting previously unselected package libpython3.13-minimal:arm64. 152s (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 ... 80185 files and directories currently installed.) 152s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_arm64.deb ... 152s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 152s Selecting previously unselected package python3.13-minimal. 152s Preparing to unpack .../python3.13-minimal_3.13.1-2_arm64.deb ... 152s Unpacking python3.13-minimal (3.13.1-2) ... 152s Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... 152s Setting up python3.13-minimal (3.13.1-2) ... 154s (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 ... 80505 files and directories currently installed.) 154s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_arm64.deb ... 154s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 154s Setting up python3-minimal (3.13.1-1~exp2) ... 154s (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 ... 80505 files and directories currently installed.) 154s Preparing to unpack .../python3_3.13.1-1~exp2_arm64.deb ... 154s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 154s Selecting previously unselected package libpython3.13-stdlib:arm64. 154s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_arm64.deb ... 154s Unpacking libpython3.13-stdlib:arm64 (3.13.1-2) ... 154s Selecting previously unselected package python3.13. 154s Preparing to unpack .../python3.13_3.13.1-2_arm64.deb ... 154s Unpacking python3.13 (3.13.1-2) ... 154s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_arm64.deb ... 154s Unpacking libpython3-stdlib:arm64 (3.13.1-1~exp2) over (3.12.8-1) ... 154s Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... 154s Setting up libpython3-stdlib:arm64 (3.13.1-1~exp2) ... 154s Setting up python3.13 (3.13.1-2) ... 155s Setting up python3 (3.13.1-1~exp2) ... 155s /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. 155s for fn in glob1(directory, "%s.*" % fname): 156s Processing triggers for man-db (2.13.0-1) ... 156s Processing triggers for systemd (257-2ubuntu1) ... 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 0 157s Starting 2 pkgProblemResolver with broken count: 0 157s Done 158s The following packages will be REMOVED: 158s python3.12* python3.12-minimal* 158s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 158s After this operation, 8710 kB disk space will be freed. 158s (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 ... 80922 files and directories currently installed.) 158s Removing python3.12 (3.12.8-3) ... 158s Removing python3.12-minimal (3.12.8-3) ... 159s /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. 159s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 159s Processing triggers for man-db (2.13.0-1) ... 159s Processing triggers for systemd (257-2ubuntu1) ... 159s (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 ... 80894 files and directories currently installed.) 159s Purging configuration files for python3.12-minimal (3.12.8-3) ... 162s autopkgtest [19:11:41]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 162s autopkgtest [19:11:41]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pdbfixer 164s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (dsc) [2196 B] 164s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (tar) [648 kB] 164s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pdbfixer 1.9-4 (diff) [3032 B] 165s gpgv: Signature made Sat Nov 16 13:59:37 2024 UTC 165s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 165s gpgv: issuer "tchet@debian.org" 165s gpgv: Can't check signature: No public key 165s dpkg-source: warning: cannot verify inline signature for ./python-pdbfixer_1.9-4.dsc: no acceptable signature found 165s autopkgtest [19:11:44]: testing package python-pdbfixer version 1.9-4 165s autopkgtest [19:11:44]: build not needed 166s autopkgtest [19:11:45]: test command1: preparing testbed 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Starting pkgProblemResolver with broken count: 0 167s Starting 2 pkgProblemResolver with broken count: 0 167s Done 168s The following NEW packages will be installed: 168s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 168s python3-iniconfig python3-legacy-cgi python3-numpy python3-openmm 168s python3-packaging python3-pdbfixer python3-pluggy python3-pytest 168s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 16.9 MB of archives. 168s After this operation, 131 MB of additional disk space will be used. 168s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 168s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 169s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 169s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-2 [987 kB] 169s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-2 [333 kB] 169s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 169s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-legacy-cgi all 2.6.1-2 [16.3 kB] 169s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 169s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openmm arm64 8.1.2+dfsg-2 [7726 kB] 169s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 169s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pdbfixer all 1.9-4 [463 kB] 169s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 169s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 170s Fetched 16.9 MB in 1s (11.7 MB/s) 170s Selecting previously unselected package libblas3:arm64. 170s (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 ... 80894 files and directories currently installed.) 170s Preparing to unpack .../00-libblas3_3.12.0-4_arm64.deb ... 170s Unpacking libblas3:arm64 (3.12.0-4) ... 170s Selecting previously unselected package libgfortran5:arm64. 170s Preparing to unpack .../01-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 170s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 170s Selecting previously unselected package liblapack3:arm64. 170s Preparing to unpack .../02-liblapack3_3.12.0-4_arm64.deb ... 170s Unpacking liblapack3:arm64 (3.12.0-4) ... 170s Selecting previously unselected package libopenmm8.1. 170s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-2_arm64.deb ... 170s Unpacking libopenmm8.1 (8.1.2+dfsg-2) ... 170s Selecting previously unselected package libopenmm-dev. 170s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-2_arm64.deb ... 170s Unpacking libopenmm-dev (8.1.2+dfsg-2) ... 170s Selecting previously unselected package python3-iniconfig. 170s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 170s Unpacking python3-iniconfig (1.1.1-2) ... 170s Selecting previously unselected package python3-legacy-cgi. 170s Preparing to unpack .../06-python3-legacy-cgi_2.6.1-2_all.deb ... 170s Unpacking python3-legacy-cgi (2.6.1-2) ... 170s Selecting previously unselected package python3-numpy. 170s Preparing to unpack .../07-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 170s Unpacking python3-numpy (1:1.26.4+ds-12) ... 171s Selecting previously unselected package python3-openmm. 171s Preparing to unpack .../08-python3-openmm_8.1.2+dfsg-2_arm64.deb ... 171s Unpacking python3-openmm (8.1.2+dfsg-2) ... 171s Selecting previously unselected package python3-packaging. 171s Preparing to unpack .../09-python3-packaging_24.2-1_all.deb ... 171s Unpacking python3-packaging (24.2-1) ... 171s Selecting previously unselected package python3-pdbfixer. 171s Preparing to unpack .../10-python3-pdbfixer_1.9-4_all.deb ... 171s Unpacking python3-pdbfixer (1.9-4) ... 171s Selecting previously unselected package python3-pluggy. 171s Preparing to unpack .../11-python3-pluggy_1.5.0-1_all.deb ... 171s Unpacking python3-pluggy (1.5.0-1) ... 171s Selecting previously unselected package python3-pytest. 171s Preparing to unpack .../12-python3-pytest_8.3.3-1_all.deb ... 171s Unpacking python3-pytest (8.3.3-1) ... 171s Setting up python3-iniconfig (1.1.1-2) ... 171s Setting up libblas3:arm64 (3.12.0-4) ... 171s 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 171s Setting up python3-packaging (24.2-1) ... 171s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 171s Setting up python3-pluggy (1.5.0-1) ... 172s Setting up python3-legacy-cgi (2.6.1-2) ... 172s Setting up libopenmm8.1 (8.1.2+dfsg-2) ... 172s Setting up liblapack3:arm64 (3.12.0-4) ... 172s 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 172s Setting up python3-pytest (8.3.3-1) ... 172s Setting up libopenmm-dev (8.1.2+dfsg-2) ... 172s Setting up python3-numpy (1:1.26.4+ds-12) ... 174s Setting up python3-openmm (8.1.2+dfsg-2) ... 174s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 174s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 174s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 174s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 174s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 174s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 174s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 174s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 174s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 174s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 174s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 174s "(?:\s*#.*$)" "|" # comments (dumped) 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 174s "(\S+)" # unquoted words 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 174s """ Tokenizer method for the mmCIF syntax file - 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 174s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 174s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 174s "(?:\s*#.*$)" "|" # comments (dumped) 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 174s "(\S+)" # unquoted words 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 174s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 174s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 174s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 174s "(?:\s*#.*$)" "|" # comments (dumped) 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 174s "(\S+)" # unquoted words 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 174s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 174s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 174s "(?:\s*#.*$)" "|" # comments (dumped) 174s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 174s "(\S+)" # unquoted words 174s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 174s pattern = re.compile('bias_(.*)_(.*)\.npy') 174s /usr/lib/python3/dist-packages/openmm/openmm.py:6593: SyntaxWarning: invalid escape sequence '\S' 174s match = re.search("<([^?]\S*)", inputString) 175s Setting up python3-pdbfixer (1.9-4) ... 175s Processing triggers for man-db (2.13.0-1) ... 175s Processing triggers for libc-bin (2.40-4ubuntu1) ... 176s autopkgtest [19:11:55]: test command1: pytest-3 pdbfixer/tests/test_removechains.py 176s autopkgtest [19:11:55]: test command1: [----------------------- 177s ============================= test session starts ============================== 177s platform linux -- Python 3.13.1, pytest-8.3.3, pluggy-1.5.0 177s rootdir: /tmp/autopkgtest.NToy0d/build.Nlb/src 177s plugins: typeguard-4.4.1 177s collected 2 items 177s 184s pdbfixer/tests/test_removechains.py .. [100%] 184s 184s =============================== warnings summary =============================== 184s :488 184s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 184s 184s :488 184s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 184s 184s :488 184s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 184s 184s pdbfixer/pdbfixer.py:58 184s /tmp/autopkgtest.NToy0d/build.Nlb/src/pdbfixer/pdbfixer.py:58: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 184s from pkg_resources import resource_filename 184s 184s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 184s ======================== 2 passed, 4 warnings in 7.28s ========================= 184s autopkgtest [19:12:03]: test command1: -----------------------] 185s command1 PASS 185s autopkgtest [19:12:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 185s autopkgtest [19:12:04]: @@@@@@@@@@@@@@@@@@@@ summary 185s command1 PASS 202s nova [W] Using flock in prodstack6-arm64 202s flock: timeout while waiting to get lock 202s Creating nova instance adt-plucky-arm64-python-pdbfixer-20250103-190859-juju-7f2275-prod-proposed-migration-environment-2-2e9c7f1b-eecd-432a-850d-7491ea7fb1a2 from image adt/ubuntu-plucky-arm64-server-20250102.img (UUID 4cb073f4-4206-4362-b576-2406cb25ddd8)... 202s nova [W] Timed out waiting for 0476baa9-3e79-4e3e-b997-29f957727e88 to get deleted.