0s autopkgtest [17:02:27]: starting date and time: 2025-10-18 17:02:27+0000 0s autopkgtest [17:02:27]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [17:02:27]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yz7bwvt4/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade gemmi --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-18.secgroup --name adt-resolute-arm64-gemmi-20251018-170227-juju-7f2275-prod-proposed-migration-environment-20-b9fa789b-6e98-49f2-812f-b4985dff04e2 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-gemmi-20251018-170227-juju-7f2275-prod-proposed-migration-environment-20-b9fa789b-6e98-49f2-812f-b4985dff04e2 from image adt/ubuntu-resolute-arm64-server-20251018.img (UUID f7a49384-4e4d-4350-9a26-1f59236f89dd)... 82s autopkgtest [17:03:49]: testbed dpkg architecture: arm64 83s autopkgtest [17:03:50]: testbed apt version: 3.1.6ubuntu2 83s autopkgtest [17:03:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 83s autopkgtest [17:03:50]: testbed release detected to be: None 84s autopkgtest [17:03:51]: updating testbed package index (apt update) 84s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 84s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 85s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 85s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [81.1 kB] 85s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [223 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 85s Fetched 831 kB in 1s (784 kB/s) 86s Reading package lists... 87s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 87s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 88s Reading package lists... 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Calculating upgrade... 89s The following packages will be upgraded: 89s apt flash-kernel gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 89s libpython3-stdlib lto-disabled-list python3 python3-minimal 89s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 2671 kB of archives. 89s After this operation, 66.6 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.13.7-2 [27.8 kB] 89s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.13.7-2 [23.9 kB] 89s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.13.7-2 [10.6 kB] 89s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.8ubuntu1 [1055 kB] 90s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.8ubuntu1 [1373 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgirepository-1.0-1 arm64 1.86.0-6 [84.5 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 gir1.2-girepository-2.0 arm64 1.86.0-6 [25.3 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 flash-kernel arm64 3.109ubuntu7 [58.8 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 lto-disabled-list all 71 [12.5 kB] 91s dpkg-preconfigure: unable to re-open stdin: No such file or directory 91s Fetched 2671 kB in 1s (2391 kB/s) 91s (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 ... 83359 files and directories currently installed.) 91s Preparing to unpack .../python3-minimal_3.13.7-2_arm64.deb ... 91s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 91s Setting up python3-minimal (3.13.7-2) ... 91s (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 ... 83359 files and directories currently installed.) 91s Preparing to unpack .../0-python3_3.13.7-2_arm64.deb ... 91s running python pre-rtupdate hooks for python3.13... 91s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 92s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_arm64.deb ... 92s Unpacking libpython3-stdlib:arm64 (3.13.7-2) over (3.13.7-1) ... 92s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_arm64.deb ... 92s Unpacking libapt-pkg7.0:arm64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 92s Preparing to unpack .../3-apt_3.1.8ubuntu1_arm64.deb ... 92s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 92s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_arm64.deb ... 92s Unpacking libgirepository-1.0-1:arm64 (1.86.0-6) over (1.84.0-1) ... 92s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_arm64.deb ... 92s Unpacking gir1.2-girepository-2.0:arm64 (1.86.0-6) over (1.84.0-1) ... 92s Preparing to unpack .../6-flash-kernel_3.109ubuntu7_arm64.deb ... 92s Unpacking flash-kernel (3.109ubuntu7) over (3.109ubuntu6) ... 93s Preparing to unpack .../7-lto-disabled-list_71_all.deb ... 93s Unpacking lto-disabled-list (71) over (69) ... 93s Setting up lto-disabled-list (71) ... 93s Setting up libgirepository-1.0-1:arm64 (1.86.0-6) ... 93s Setting up libapt-pkg7.0:arm64 (3.1.8ubuntu1) ... 93s Setting up libpython3-stdlib:arm64 (3.13.7-2) ... 93s Setting up apt (3.1.8ubuntu1) ... 93s Setting up python3 (3.13.7-2) ... 93s running python rtupdate hooks for python3.13... 93s running python post-rtupdate hooks for python3.13... 93s Setting up gir1.2-girepository-2.0:arm64 (1.86.0-6) ... 93s Setting up flash-kernel (3.109ubuntu7) ... 94s flash-kernel: deferring update (trigger activated) 94s Processing triggers for libc-bin (2.42-0ubuntu3) ... 94s Processing triggers for man-db (2.13.1-1) ... 96s Processing triggers for initramfs-tools (0.150ubuntu3) ... 96s update-initramfs: Generating /boot/initrd.img-6.17.0-5-generic 119s System running in EFI mode, skipping. 119s Processing triggers for flash-kernel (3.109ubuntu7) ... 119s System running in EFI mode, skipping. 119s autopkgtest [17:04:26]: upgrading testbed (apt dist-upgrade and autopurge) 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [17:04:30]: rebooting testbed after setup commands that affected boot 152s autopkgtest [17:04:59]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 154s autopkgtest [17:05:01]: @@@@@@@@@@@@@@@@@@@@ apt-source gemmi 158s Get:1 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (dsc) [2280 B] 158s Get:2 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (tar) [1290 kB] 158s Get:3 http://ftpmaster.internal/ubuntu resolute/universe gemmi 0.6.5+ds-3 (diff) [7464 B] 159s gpgv: Signature made Mon Feb 3 14:50:02 2025 UTC 159s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 159s gpgv: issuer "merkys@debian.org" 159s gpgv: Can't check signature: No public key 159s dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: no acceptable signature found 159s autopkgtest [17:05:06]: testing package gemmi version 0.6.5+ds-3 159s autopkgtest [17:05:06]: build not needed 162s autopkgtest [17:05:09]: test command1: preparing testbed 162s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Solving dependencies... 163s The following NEW packages will be installed: 163s gemmi gemmi-dev libblas3 libgfortran5 liblapack3 python3-gemmi 163s python3-iniconfig python3-numpy python3-numpy-dev python3-packaging 163s python3-pluggy python3-pytest tao-pegtl-dev 163s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 12.0 MB of archives. 163s After this operation, 48.0 MB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 164s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 164s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 164s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 165s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 167s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 gemmi arm64 0.6.5+ds-3 [1069 kB] 168s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 tao-pegtl-dev all 3.2.7-1 [59.6 kB] 168s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 gemmi-dev arm64 0.6.5+ds-3 [1203 kB] 169s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gemmi arm64 0.6.5+ds-3 [2206 kB] 170s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 170s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 170s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 170s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 8.3.5-2 [252 kB] 170s Fetched 12.0 MB in 7s (1817 kB/s) 170s Selecting previously unselected package python3-numpy-dev: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 ... 83359 files and directories currently installed.) 170s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 170s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 170s Selecting previously unselected package libblas3:arm64. 170s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 170s Unpacking libblas3:arm64 (3.12.1-6build1) ... 170s Selecting previously unselected package libgfortran5:arm64. 170s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 170s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 170s Selecting previously unselected package liblapack3:arm64. 170s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 170s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 171s Selecting previously unselected package python3-numpy. 171s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 171s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 171s Selecting previously unselected package gemmi. 171s Preparing to unpack .../05-gemmi_0.6.5+ds-3_arm64.deb ... 171s Unpacking gemmi (0.6.5+ds-3) ... 171s Selecting previously unselected package tao-pegtl-dev. 171s Preparing to unpack .../06-tao-pegtl-dev_3.2.7-1_all.deb ... 171s Unpacking tao-pegtl-dev (3.2.7-1) ... 171s Selecting previously unselected package gemmi-dev. 171s Preparing to unpack .../07-gemmi-dev_0.6.5+ds-3_arm64.deb ... 171s Unpacking gemmi-dev (0.6.5+ds-3) ... 171s Selecting previously unselected package python3-gemmi. 171s Preparing to unpack .../08-python3-gemmi_0.6.5+ds-3_arm64.deb ... 171s Unpacking python3-gemmi (0.6.5+ds-3) ... 171s Selecting previously unselected package python3-iniconfig. 171s Preparing to unpack .../09-python3-iniconfig_1.1.1-2_all.deb ... 171s Unpacking python3-iniconfig (1.1.1-2) ... 171s Selecting previously unselected package python3-packaging. 171s Preparing to unpack .../10-python3-packaging_25.0-1_all.deb ... 171s Unpacking python3-packaging (25.0-1) ... 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_8.3.5-2_all.deb ... 171s Unpacking python3-pytest (8.3.5-2) ... 171s Setting up python3-iniconfig (1.1.1-2) ... 171s Setting up python3-gemmi (0.6.5+ds-3) ... 171s Setting up libblas3:arm64 (3.12.1-6build1) ... 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 (25.0-1) ... 172s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 172s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 172s Setting up python3-pluggy (1.5.0-1) ... 172s Setting up gemmi (0.6.5+ds-3) ... 172s Setting up tao-pegtl-dev (3.2.7-1) ... 172s Setting up liblapack3:arm64 (3.12.1-6build1) ... 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 (8.3.5-2) ... 172s Setting up gemmi-dev (0.6.5+ds-3) ... 172s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 174s Processing triggers for man-db (2.13.1-1) ... 175s Processing triggers for libc-bin (2.42-0ubuntu3) ... 176s autopkgtest [17:05:23]: test command1: pytest-3 -k 'not test_sfcalc_ and not test_sfcalc4' 176s autopkgtest [17:05:23]: test command1: [----------------------- 177s ........................................................................ [ 38%] 178s .............................s.................s..............ssssss.... [ 76%] 178s ............................................ [100%] 178s =========================== short test summary info ============================ 178s SKIPPED [1] tests/test_mol.py:535: BioPython not installed. 178s SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. 178s SKIPPED [1] tests/test_seq.py:127: BioPython not installed. 178s SKIPPED [1] tests/test_seq.py:132: BioPython not installed. 178s SKIPPED [1] tests/test_seq.py:139: BioPython not installed. 178s SKIPPED [1] tests/test_seq.py:146: BioPython not installed. 178s SKIPPED [1] tests/test_seq.py:105: BioPython not installed. 178s SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 178s 180 passed, 8 skipped, 3 deselected in 1.14s 178s autopkgtest [17:05:25]: test command1: -----------------------] 179s autopkgtest [17:05:26]: test command1: - - - - - - - - - - results - - - - - - - - - - 179s command1 PASS 179s autopkgtest [17:05:26]: @@@@@@@@@@@@@@@@@@@@ summary 179s command1 PASS