0s autopkgtest [05:21:51]: starting date and time: 2025-10-24 05:21:51+0000 0s autopkgtest [05:21:51]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [05:21:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5wx1ta25/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-1.secgroup --name adt-resolute-amd64-openmm-20251024-052151-juju-7f2275-prod-proposed-migration-environment-2-0c0d2c77-c2b6-48bf-9ce5-a4238a2a518b --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-openmm-20251024-052151-juju-7f2275-prod-proposed-migration-environment-2-0c0d2c77-c2b6-48bf-9ce5-a4238a2a518b from image adt/ubuntu-resolute-amd64-server-20251024.img (UUID 310022dd-8dd9-48c7-a816-c2d8419ef402)... 32s autopkgtest [05:22:23]: testbed dpkg architecture: amd64 33s autopkgtest [05:22:24]: testbed apt version: 3.1.8ubuntu1 33s autopkgtest [05:22:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [05:22:24]: testbed release detected to be: None 34s autopkgtest [05:22:25]: updating testbed package index (apt update) 34s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 34s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 34s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 34s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 34s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [61.6 kB] 34s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 34s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [533 kB] 34s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 34s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [147 kB] 34s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [97.2 kB] 34s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3040 B] 34s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 34s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 35s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 35s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [145 kB] 35s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [385 kB] 35s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [10.8 kB] 35s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 35s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 35s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [492 B] 35s Fetched 1532 kB in 1s (1488 kB/s) 36s Reading package lists... 36s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 36s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 37s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 37s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 37s Reading package lists... 37s Reading package lists... 37s Building dependency tree... 37s Reading state information... 37s Calculating upgrade... 37s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 37s autopkgtest [05:22:28]: upgrading testbed (apt dist-upgrade and autopurge) 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Calculating upgrade... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Solving dependencies... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 41s autopkgtest [05:22:32]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 41s autopkgtest [05:22:32]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 45s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11build1 (dsc) [2578 B] 45s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11build1 (tar) [11.5 MB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11build1 (diff) [23.4 kB] 45s gpgv: Signature made Mon Oct 20 14:19:01 2025 UTC 45s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 45s gpgv: Can't check signature: No public key 45s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-11build1.dsc: no acceptable signature found 45s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 45s autopkgtest [05:22:36]: testing package openmm version 8.1.2+dfsg-11build1 46s autopkgtest [05:22:37]: build not needed 52s autopkgtest [05:22:43]: test test-python: preparing testbed 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Solving dependencies... 52s The following NEW packages will be installed: 52s cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu gcc gcc-15 52s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 libcc1-0 52s libgcc-15-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 liblapack3 52s liblsan0 libmpc3 libopenmm-dev libopenmm8.1 libquadmath0 libtsan2 libubsan1 52s python3-all python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 52s python3-packaging python3-pluggy python3-pytest 52s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 71.9 MB of archives. 52s After this operation, 306 MB of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 52s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 52s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 53s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 53s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1 [685 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-1build3 [57.0 kB] 53s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-5ubuntu1 [12.9 MB] 54s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-5ubuntu1 [1028 B] 54s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 54s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 54s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-5ubuntu1 [47.4 kB] 54s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 54s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-5ubuntu1 [29.3 kB] 54s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-5ubuntu1 [3071 kB] 54s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-5ubuntu1 [1360 kB] 54s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-5ubuntu1 [2757 kB] 54s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-5ubuntu1 [1210 kB] 55s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-5ubuntu1 [1685 kB] 55s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-5ubuntu1 [153 kB] 55s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-5ubuntu1 [2863 kB] 55s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-5ubuntu1 [25.4 MB] 56s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-5ubuntu1 [523 kB] 56s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 56s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 56s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-11build1 [1046 kB] 56s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-11build1 [342 kB] 56s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 56s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 56s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-openmm amd64 8.1.2+dfsg-11build1 [7756 kB] 56s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 56s Get:32 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 56s Get:33 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-pytest all 8.4.2-1 [268 kB] 57s Fetched 71.9 MB in 4s (17.8 MB/s) 57s Selecting previously unselected package python3-numpy-dev:amd64. 57s (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 ... 78459 files and directories currently installed.) 57s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 57s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 57s Selecting previously unselected package libblas3:amd64. 57s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 57s Unpacking libblas3:amd64 (3.12.1-6build1) ... 57s Selecting previously unselected package libgfortran5:amd64. 57s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package liblapack3:amd64. 57s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 57s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 57s Selecting previously unselected package python3-numpy. 57s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 57s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 57s Selecting previously unselected package libisl23:amd64. 57s Preparing to unpack .../05-libisl23_0.27-1_amd64.deb ... 57s Unpacking libisl23:amd64 (0.27-1) ... 57s Selecting previously unselected package libmpc3:amd64. 57s Preparing to unpack .../06-libmpc3_1.3.1-1build3_amd64.deb ... 57s Unpacking libmpc3:amd64 (1.3.1-1build3) ... 57s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 57s Preparing to unpack .../07-cpp-15-x86-64-linux-gnu_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package cpp-15. 57s Preparing to unpack .../08-cpp-15_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking cpp-15 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package cpp-x86-64-linux-gnu. 57s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 57s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 57s Selecting previously unselected package cpp. 57s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 57s Unpacking cpp (4:15.2.0-4ubuntu1) ... 57s Selecting previously unselected package libcc1-0:amd64. 57s Preparing to unpack .../11-libcc1-0_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libcc1-0:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libgomp1:amd64. 57s Preparing to unpack .../12-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libitm1:amd64. 57s Preparing to unpack .../13-libitm1_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libitm1:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libasan8:amd64. 57s Preparing to unpack .../14-libasan8_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libasan8:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package liblsan0:amd64. 57s Preparing to unpack .../15-liblsan0_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking liblsan0:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libtsan2:amd64. 57s Preparing to unpack .../16-libtsan2_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libtsan2:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libubsan1:amd64. 57s Preparing to unpack .../17-libubsan1_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libubsan1:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libhwasan0:amd64. 57s Preparing to unpack .../18-libhwasan0_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libhwasan0:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libquadmath0:amd64. 57s Preparing to unpack .../19-libquadmath0_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libquadmath0:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package libgcc-15-dev:amd64. 57s Preparing to unpack .../20-libgcc-15-dev_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking libgcc-15-dev:amd64 (15.2.0-5ubuntu1) ... 57s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 57s Preparing to unpack .../21-gcc-15-x86-64-linux-gnu_15.2.0-5ubuntu1_amd64.deb ... 57s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 58s Selecting previously unselected package gcc-15. 58s Preparing to unpack .../22-gcc-15_15.2.0-5ubuntu1_amd64.deb ... 58s Unpacking gcc-15 (15.2.0-5ubuntu1) ... 58s Selecting previously unselected package gcc-x86-64-linux-gnu. 58s Preparing to unpack .../23-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 58s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 58s Selecting previously unselected package gcc. 58s Preparing to unpack .../24-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 58s Unpacking gcc (4:15.2.0-4ubuntu1) ... 58s Selecting previously unselected package libopenmm8.1. 58s Preparing to unpack .../25-libopenmm8.1_8.1.2+dfsg-11build1_amd64.deb ... 58s Unpacking libopenmm8.1 (8.1.2+dfsg-11build1) ... 58s Selecting previously unselected package libopenmm-dev. 58s Preparing to unpack .../26-libopenmm-dev_8.1.2+dfsg-11build1_amd64.deb ... 58s Unpacking libopenmm-dev (8.1.2+dfsg-11build1) ... 58s Selecting previously unselected package python3-all. 58s Preparing to unpack .../27-python3-all_3.13.7-1_amd64.deb ... 58s Unpacking python3-all (3.13.7-1) ... 58s Selecting previously unselected package python3-iniconfig. 58s Preparing to unpack .../28-python3-iniconfig_1.1.1-2_all.deb ... 58s Unpacking python3-iniconfig (1.1.1-2) ... 58s Selecting previously unselected package python3-openmm. 58s Preparing to unpack .../29-python3-openmm_8.1.2+dfsg-11build1_amd64.deb ... 58s Unpacking python3-openmm (8.1.2+dfsg-11build1) ... 58s Selecting previously unselected package python3-packaging. 58s Preparing to unpack .../30-python3-packaging_25.0-1_all.deb ... 58s Unpacking python3-packaging (25.0-1) ... 58s Selecting previously unselected package python3-pluggy. 58s Preparing to unpack .../31-python3-pluggy_1.6.0-1_all.deb ... 58s Unpacking python3-pluggy (1.6.0-1) ... 58s Selecting previously unselected package python3-pytest. 58s Preparing to unpack .../32-python3-pytest_8.4.2-1_all.deb ... 58s Unpacking python3-pytest (8.4.2-1) ... 58s Setting up python3-iniconfig (1.1.1-2) ... 58s Setting up python3-all (3.13.7-1) ... 58s Setting up libgomp1:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libblas3:amd64 (3.12.1-6build1) ... 58s 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 58s Setting up python3-packaging (25.0-1) ... 58s Setting up libquadmath0:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libmpc3:amd64 (1.3.1-1build3) ... 58s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 58s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 58s Setting up python3-pluggy (1.6.0-1) ... 58s Setting up libubsan1:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libhwasan0:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libasan8:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libtsan2:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libisl23:amd64 (0.27-1) ... 58s Setting up libopenmm8.1 (8.1.2+dfsg-11build1) ... 58s Setting up libcc1-0:amd64 (15.2.0-5ubuntu1) ... 58s Setting up liblsan0:amd64 (15.2.0-5ubuntu1) ... 58s Setting up libitm1:amd64 (15.2.0-5ubuntu1) ... 58s Setting up liblapack3:amd64 (3.12.1-6build1) ... 58s 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 58s Setting up libgcc-15-dev:amd64 (15.2.0-5ubuntu1) ... 58s Setting up python3-pytest (8.4.2-1) ... 58s Setting up cpp-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 58s Setting up libopenmm-dev (8.1.2+dfsg-11build1) ... 58s Setting up gcc-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 58s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 59s Setting up python3-openmm (8.1.2+dfsg-11build1) ... 60s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 60s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 60s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 60s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 60s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 60s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 60s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 60s "(?:\s*#.*$)" "|" # comments (dumped) 60s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 60s "(\S+)" # unquoted words 60s Setting up cpp-15 (15.2.0-5ubuntu1) ... 60s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 60s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 60s Setting up gcc-15 (15.2.0-5ubuntu1) ... 60s Setting up cpp (4:15.2.0-4ubuntu1) ... 60s Setting up gcc (4:15.2.0-4ubuntu1) ... 60s Processing triggers for man-db (2.13.1-1) ... 60s Processing triggers for libc-bin (2.42-0ubuntu3) ... 61s autopkgtest [05:22:52]: test test-python: [----------------------- 62s ============================= test session starts ============================== 62s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 62s rootdir: /tmp/autopkgtest.8yyesy/build.hFa/src/wrappers/python/tests 62s configfile: pytest.ini 62s plugins: typeguard-4.4.2 62s collected 327 items 62s 62s TestAPIUnits.py .................................. [ 10%] 62s TestATMForce.py . [ 10%] 62s TestAmberInpcrdFile.py .....s [ 12%] 67s TestAmberPrmtopFile.py ....................... [ 19%] 67s TestBytes.py . [ 19%] 85s TestCharmmFiles.py ....s..........s......... [ 27%] 85s TestCheckpointReporter.py . [ 27%] 85s TestDcdFile.py ... [ 28%] 86s TestDesmondDMSFile.py ....... [ 30%] 86s TestElement.py .... [ 32%] 99s TestForceField.py s........................................ss..s.. [ 46%] 99s TestForceGroups.py ... [ 47%] 99s TestGenerators.py .. [ 48%] 99s TestGromacsGroFile.py . [ 48%] 99s TestGromacsTopFile.py sssssssssssss [ 52%] 532s TestIntegrators.py .s..... [ 54%] 533s TestMetadynamics.py . [ 55%] 553s TestModeller.py .............s............. [ 63%] 553s TestNumpyCompatibility.py ......... [ 66%] 553s TestPatches.py ..... [ 67%] 557s TestPdbFile.py ...... [ 69%] 560s TestPdbReporter.py ........ [ 71%] 562s TestPdbxFile.py ....... [ 74%] 562s TestPickle.py ... [ 74%] 564s TestSimulatedTempering.py .. [ 75%] 593s TestSimulation.py ....... [ 77%] 593s TestStateDataReporter.py . [ 77%] 593s TestSwigWrappers.py . [ 78%] 593s TestTopology.py ... [ 79%] 593s TestUnitCell.py .. [ 79%] 593s TestUnits.py ...................................................... [ 96%] 593s TestVec3.py ....... [ 98%] 593s TestXtcFile.py ..... [100%] 593s 593s =============================== warnings summary =============================== 593s :488 593s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 593s 593s :488 593s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 593s 593s :488 593s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 593s 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 593s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 593s warnings.warn( 593s 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 593s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 593s warnings.warn( 593s 593s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 593s =========== 305 passed, 22 skipped, 10 warnings in 531.58s (0:08:51) =========== 594s autopkgtest [05:31:45]: test test-python: -----------------------] 594s test-python PASS 594s autopkgtest [05:31:45]: test test-python: - - - - - - - - - - results - - - - - - - - - - 594s autopkgtest [05:31:45]: @@@@@@@@@@@@@@@@@@@@ summary 594s test-python PASS