0s autopkgtest [02:11:45]: starting date and time: 2026-02-06 02:11:45+0000 0s autopkgtest [02:11:45]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [02:11:45]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mtmwr0gx/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.160 lxd-armhf-10.145.243.160:autopkgtest/ubuntu/resolute/armhf 26s autopkgtest [02:12:11]: testbed dpkg architecture: armhf 28s autopkgtest [02:12:13]: testbed apt version: 3.1.14 32s autopkgtest [02:12:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 34s autopkgtest [02:12:19]: testbed release detected to be: None 42s autopkgtest [02:12:27]: updating testbed package index (apt update) 44s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 45s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 45s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 45s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 45s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.4 kB] 45s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [221 kB] 45s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 45s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1631 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [255 kB] 47s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1333 kB] 48s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7492 B] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 54s Get:13 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [310 kB] 54s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1399 kB] 55s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1373 kB] 55s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.1 MB] 57s Get:17 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [176 kB] 58s Fetched 43.7 MB in 15s (2973 kB/s) 60s Reading package lists... 66s autopkgtest [02:12:51]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 69s The following packages will be upgraded: 69s libc-bin libc-gconv-modules-extra libc6 libdrm-amdgpu1 libdrm-common libdrm2 69s locales mawk 69s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 8039 kB of archives. 69s After this operation, 0 B of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 69s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 69s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 69s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf mawk armhf 1.3.4.20260129-1 [120 kB] 69s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 70s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm-common all 2.4.131-1 [9774 B] 70s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm2 armhf 2.4.131-1 [38.0 kB] 70s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libdrm-amdgpu1 armhf 2.4.131-1 [20.9 kB] 70s Preconfiguring packages ... 70s Fetched 8039 kB in 1s (8090 kB/s) 71s (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 ... 68395 files and directories currently installed.) 71s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 71s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 71s (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 ... 68395 files and directories currently installed.) 71s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 71s readlink: /usr/lib/libeatmydata: No such file or directory 71s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc6:armhf (2.42-2ubuntu5) ... 71s (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 ... 68395 files and directories currently installed.) 71s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 71s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 71s Setting up libc-bin (2.42-2ubuntu5) ... 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 ... 68395 files and directories currently installed.) 72s Preparing to unpack .../mawk_1.3.4.20260129-1_armhf.deb ... 72s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 72s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 72s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 72s Preparing to unpack .../libdrm-common_2.4.131-1_all.deb ... 72s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 72s Preparing to unpack .../libdrm2_2.4.131-1_armhf.deb ... 72s Unpacking libdrm2:armhf (2.4.131-1) over (2.4.129-1) ... 72s Preparing to unpack .../libdrm-amdgpu1_2.4.131-1_armhf.deb ... 72s Unpacking libdrm-amdgpu1:armhf (2.4.131-1) over (2.4.129-1) ... 72s Setting up locales (2.42-2ubuntu5) ... 73s Generating locales (this might take a while)... 75s en_US.UTF-8... done 75s Generation complete. 75s Setting up mawk (1.3.4.20260129-1) ... 75s Setting up libdrm-common (2.4.131-1) ... 75s Setting up libdrm2:armhf (2.4.131-1) ... 75s Setting up libdrm-amdgpu1:armhf (2.4.131-1) ... 75s Processing triggers for systemd (259-1ubuntu3) ... 76s Processing triggers for man-db (2.13.1-1) ... 77s Processing triggers for libc-bin (2.42-2ubuntu5) ... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s Solving dependencies... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s autopkgtest [02:13:07]: rebooting testbed after setup commands that affected boot 125s autopkgtest [02:13:50]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 151s autopkgtest [02:14:16]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 175s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (dsc) [2579 B] 175s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (tar) [11.5 MB] 175s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (diff) [23.7 kB] 175s gpgv: Signature made Mon Sep 29 08:59:53 2025 UTC 175s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 175s gpgv: issuer "merkys@debian.org" 175s gpgv: Can't check signature: No public key 175s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-12.dsc: no acceptable signature found 176s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 176s autopkgtest [02:14:41]: testing package openmm version 8.1.2+dfsg-12 180s autopkgtest [02:14:45]: build not needed 186s autopkgtest [02:14:51]: test test-python: preparing testbed 188s Reading package lists... 188s Building dependency tree... 188s Reading state information... 188s Solving dependencies... 189s The following NEW packages will be installed: 189s cpp cpp-15 cpp-15-arm-linux-gnueabihf cpp-arm-linux-gnueabihf gcc gcc-15 189s gcc-15-arm-linux-gnueabihf gcc-arm-linux-gnueabihf libasan8 libblas3 189s libcc1-0 libgcc-15-dev libgfortran5 libgomp1 libisl23 liblapack3 libmpc3 189s libopenmm-dev libopenmm8.1 libpython3.14-minimal libpython3.14-stdlib 189s libubsan1 python3-all python3-iniconfig python3-numpy python3-numpy-dev 189s python3-openmm python3-pluggy python3-pytest python3.14 python3.14-minimal 189s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 58.8 MB of archives. 189s After this operation, 237 MB of additional disk space will be used. 189s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.3.5+ds-3 [141 kB] 189s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 189s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 189s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 189s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.3.5+ds-3 [4729 kB] 190s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.2-1 [905 kB] 190s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.2-1 [2155 kB] 190s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 190s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 190s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 190s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 190s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 190s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 190s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 190s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 190s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 190s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 190s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 190s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 191s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 191s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 191s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 191s Get:23 http://ftpmaster.internal/ubuntu resolute/universe armhf libopenmm8.1 armhf 8.1.2+dfsg-12 [969 kB] 191s Get:24 http://ftpmaster.internal/ubuntu resolute/universe armhf libopenmm-dev armhf 8.1.2+dfsg-12 [335 kB] 191s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.2-1 [2270 kB] 191s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.2-1 [816 kB] 191s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf python3-all armhf 3.13.9-3 [890 B] 191s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 2.1.0-2 [6962 B] 191s Get:29 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-openmm armhf 8.1.2+dfsg-12 [7690 kB] 191s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-2 [21.1 kB] 192s Get:31 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 9.0.2-2 [277 kB] 192s Fetched 58.8 MB in 3s (18.7 MB/s) 192s Selecting previously unselected package python3-numpy-dev:armhf. 192s (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 ... 68395 files and directories currently installed.) 192s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_armhf.deb ... 192s Unpacking python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 192s Selecting previously unselected package libblas3:armhf. 192s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_armhf.deb ... 192s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 192s Selecting previously unselected package libgfortran5:armhf. 192s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 192s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 192s Selecting previously unselected package liblapack3:armhf. 192s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_armhf.deb ... 192s Unpacking liblapack3:armhf (3.12.1-7ubuntu1) ... 193s Selecting previously unselected package python3-numpy. 193s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_armhf.deb ... 193s Unpacking python3-numpy (1:2.3.5+ds-3) ... 193s Selecting previously unselected package libpython3.14-minimal:armhf. 193s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_armhf.deb ... 193s Unpacking libpython3.14-minimal:armhf (3.14.2-1) ... 193s Selecting previously unselected package python3.14-minimal. 193s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_armhf.deb ... 193s Unpacking python3.14-minimal (3.14.2-1) ... 193s Selecting previously unselected package libisl23:armhf. 193s Preparing to unpack .../07-libisl23_0.27-1build1_armhf.deb ... 193s Unpacking libisl23:armhf (0.27-1build1) ... 193s Selecting previously unselected package libmpc3:armhf. 193s Preparing to unpack .../08-libmpc3_1.3.1-2_armhf.deb ... 193s Unpacking libmpc3:armhf (1.3.1-2) ... 193s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 193s Preparing to unpack .../09-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 193s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 193s Selecting previously unselected package cpp-15. 193s Preparing to unpack .../10-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 193s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 193s Selecting previously unselected package cpp-arm-linux-gnueabihf. 194s Preparing to unpack .../11-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 194s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 194s Selecting previously unselected package cpp. 194s Preparing to unpack .../12-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 194s Unpacking cpp (4:15.2.0-4ubuntu1) ... 194s Selecting previously unselected package libcc1-0:armhf. 194s Preparing to unpack .../13-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package libgomp1:armhf. 194s Preparing to unpack .../14-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package libasan8:armhf. 194s Preparing to unpack .../15-libasan8_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package libubsan1:armhf. 194s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package libgcc-15-dev:armhf. 194s Preparing to unpack .../17-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 194s Preparing to unpack .../18-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package gcc-15. 194s Preparing to unpack .../19-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 194s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 194s Selecting previously unselected package gcc-arm-linux-gnueabihf. 194s Preparing to unpack .../20-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 194s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 194s Selecting previously unselected package gcc. 194s Preparing to unpack .../21-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 194s Unpacking gcc (4:15.2.0-4ubuntu1) ... 194s Selecting previously unselected package libopenmm8.1. 194s Preparing to unpack .../22-libopenmm8.1_8.1.2+dfsg-12_armhf.deb ... 194s Unpacking libopenmm8.1 (8.1.2+dfsg-12) ... 194s Selecting previously unselected package libopenmm-dev. 195s Preparing to unpack .../23-libopenmm-dev_8.1.2+dfsg-12_armhf.deb ... 195s Unpacking libopenmm-dev (8.1.2+dfsg-12) ... 195s Selecting previously unselected package libpython3.14-stdlib:armhf. 195s Preparing to unpack .../24-libpython3.14-stdlib_3.14.2-1_armhf.deb ... 195s Unpacking libpython3.14-stdlib:armhf (3.14.2-1) ... 195s Selecting previously unselected package python3.14. 195s Preparing to unpack .../25-python3.14_3.14.2-1_armhf.deb ... 195s Unpacking python3.14 (3.14.2-1) ... 195s Selecting previously unselected package python3-all. 195s Preparing to unpack .../26-python3-all_3.13.9-3_armhf.deb ... 195s Unpacking python3-all (3.13.9-3) ... 195s Selecting previously unselected package python3-iniconfig. 195s Preparing to unpack .../27-python3-iniconfig_2.1.0-2_all.deb ... 195s Unpacking python3-iniconfig (2.1.0-2) ... 195s Selecting previously unselected package python3-openmm. 195s Preparing to unpack .../28-python3-openmm_8.1.2+dfsg-12_armhf.deb ... 195s Unpacking python3-openmm (8.1.2+dfsg-12) ... 195s Selecting previously unselected package python3-pluggy. 195s Preparing to unpack .../29-python3-pluggy_1.6.0-2_all.deb ... 195s Unpacking python3-pluggy (1.6.0-2) ... 195s Selecting previously unselected package python3-pytest. 195s Preparing to unpack .../30-python3-pytest_9.0.2-2_all.deb ... 195s Unpacking python3-pytest (9.0.2-2) ... 195s Setting up python3-iniconfig (2.1.0-2) ... 196s Setting up libpython3.14-minimal:armhf (3.14.2-1) ... 196s Setting up libgomp1:armhf (15.2.0-12ubuntu1) ... 196s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 196s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 196s Setting up libmpc3:armhf (1.3.1-2) ... 196s Setting up python3-numpy-dev:armhf (1:2.3.5+ds-3) ... 196s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 196s Setting up python3-pluggy (1.6.0-2) ... 196s Setting up libubsan1:armhf (15.2.0-12ubuntu1) ... 196s Setting up libasan8:armhf (15.2.0-12ubuntu1) ... 196s Setting up libisl23:armhf (0.27-1build1) ... 196s Setting up libopenmm8.1 (8.1.2+dfsg-12) ... 196s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 196s Setting up python3.14-minimal (3.14.2-1) ... 197s Setting up libcc1-0:armhf (15.2.0-12ubuntu1) ... 197s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 197s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 197s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 197s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 197s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 197s Setting up libpython3.14-stdlib:armhf (3.14.2-1) ... 197s Setting up python3-pytest (9.0.2-2) ... 198s Setting up libopenmm-dev (8.1.2+dfsg-12) ... 198s Setting up python3-numpy (1:2.3.5+ds-3) ... 202s Setting up python3-openmm (8.1.2+dfsg-12) ... 202s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 202s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 202s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 202s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 202s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 202s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 202s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 202s "(?:\s*#.*$)" "|" # comments (dumped) 202s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 202s "(\S+)" # unquoted words 203s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 203s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 203s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 203s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 203s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 203s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 203s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 203s "(?:\s*#.*$)" "|" # comments (dumped) 203s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 203s "(\S+)" # unquoted words 203s Setting up cpp-15 (15.2.0-12ubuntu1) ... 203s Setting up cpp (4:15.2.0-4ubuntu1) ... 203s Setting up python3.14 (3.14.2-1) ... 204s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 204s Setting up python3-all (3.13.9-3) ... 204s Setting up gcc-15 (15.2.0-12ubuntu1) ... 204s Setting up gcc (4:15.2.0-4ubuntu1) ... 204s Processing triggers for systemd (259-1ubuntu3) ... 204s Processing triggers for man-db (2.13.1-1) ... 205s Processing triggers for libc-bin (2.42-2ubuntu5) ... 216s autopkgtest [02:15:21]: test test-python: [----------------------- 220s ============================= test session starts ============================== 220s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 220s rootdir: /tmp/autopkgtest.Hm7SjA/build.wVP/src/wrappers/python/tests 220s configfile: pytest.ini 220s plugins: typeguard-4.4.4 220s collected 327 items 220s 220s TestAPIUnits.py .................................. [ 10%] 220s TestATMForce.py . [ 10%] 220s TestAmberInpcrdFile.py .....s [ 12%] 231s TestAmberPrmtopFile.py ....................... [ 19%] 231s TestBytes.py . [ 19%] 254s TestCharmmFiles.py ....s..........s......... [ 27%] 257s TestCheckpointReporter.py . [ 27%] 257s TestDcdFile.py ... [ 28%] 257s TestDesmondDMSFile.py ....... [ 30%] 257s TestElement.py .... [ 32%] 278s TestForceField.py s........................................ss..s.. [ 46%] 278s TestForceGroups.py ... [ 47%] 278s TestGenerators.py .. [ 48%] 278s TestGromacsGroFile.py . [ 48%] 278s TestGromacsTopFile.py sssssssssssss [ 52%] 1018s TestIntegrators.py .s..... [ 54%] 1020s TestMetadynamics.py . [ 55%] 1060s TestModeller.py .............s............. [ 63%] 1060s TestNumpyCompatibility.py ......... [ 66%] 1060s TestPatches.py ..... [ 67%] 1065s TestPdbFile.py ...... [ 69%] 1071s TestPdbReporter.py ........ [ 71%] 1074s TestPdbxFile.py ....... [ 74%] 1075s TestPickle.py ... [ 74%] 1078s TestSimulatedTempering.py .. [ 75%] 1126s TestSimulation.py ....... [ 77%] 1126s TestStateDataReporter.py . [ 77%] 1126s TestSwigWrappers.py . [ 78%] 1126s TestTopology.py ... [ 79%] 1126s TestUnitCell.py .. [ 79%] 1126s TestUnits.py ...................................................... [ 96%] 1126s TestVec3.py ....... [ 98%] 1127s TestXtcFile.py ..... [100%] 1127s 1127s =============================== warnings summary =============================== 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1127s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 1127s warnings.warn( 1127s 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 1127s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 1127s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 1127s warnings.warn( 1127s 1127s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1127s =========== 305 passed, 22 skipped, 7 warnings in 907.81s (0:15:07) ============ 1129s ============================= test session starts ============================== 1129s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 1129s rootdir: /tmp/autopkgtest.Hm7SjA/build.wVP/src/wrappers/python/tests 1129s configfile: pytest.ini 1129s plugins: typeguard-4.4.4 1129s collected 327 items 1129s 1129s TestAPIUnits.py .................................. [ 10%] 1129s TestATMForce.py . [ 10%] 1129s TestAmberInpcrdFile.py .....s [ 12%] 1141s TestAmberPrmtopFile.py ....................... [ 19%] 1141s TestBytes.py . [ 19%] 1172s TestCharmmFiles.py ....s..........s......... [ 27%] 1172s TestCheckpointReporter.py . [ 27%] 1172s TestDcdFile.py ... [ 28%] 1175s TestDesmondDMSFile.py ....... [ 30%] 1175s TestElement.py .... [ 32%] 1200s TestForceField.py s........................................ss..s.. [ 46%] 1201s TestForceGroups.py ... [ 47%] 1201s TestGenerators.py .. [ 48%] 1201s TestGromacsGroFile.py . [ 48%] 1201s TestGromacsTopFile.py sssssssssssss [ 52%] 1974s TestIntegrators.py .s..... [ 54%] 1975s TestMetadynamics.py . [ 55%] 2019s TestModeller.py .............s............. [ 63%] 2019s TestNumpyCompatibility.py ......... [ 66%] 2019s TestPatches.py ..... [ 67%] 2026s TestPdbFile.py ...... [ 69%] 2032s TestPdbReporter.py ........ [ 71%] 2035s TestPdbxFile.py ....... [ 74%] 2036s TestPickle.py ... [ 74%] 2039s TestSimulatedTempering.py .. [ 75%] 2086s TestSimulation.py ....... [ 77%] 2087s TestStateDataReporter.py . [ 77%] 2087s TestSwigWrappers.py . [ 78%] 2087s TestTopology.py ... [ 79%] 2087s TestUnitCell.py .. [ 79%] 2087s TestUnits.py ...................................................... [ 96%] 2087s TestVec3.py ....... [ 98%] 2087s TestXtcFile.py ..... [100%] 2087s 2087s =============================== warnings summary =============================== 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 2087s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 2087s warnings.warn( 2087s 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 2087s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 2087s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 2087s warnings.warn( 2087s 2087s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 2087s =========== 305 passed, 22 skipped, 7 warnings in 959.15s (0:15:59) ============ 2088s autopkgtest [02:46:33]: test test-python: -----------------------] 2092s autopkgtest [02:46:37]: test test-python: - - - - - - - - - - results - - - - - - - - - - 2092s test-python PASS 2096s autopkgtest [02:46:41]: @@@@@@@@@@@@@@@@@@@@ summary 2096s test-python PASS