0s autopkgtest [12:00:50]: starting date and time: 2026-01-24 12:00:50+0000 0s autopkgtest [12:00:50]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:00:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pq4nl040/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade openstructure --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-15.secgroup --name adt-resolute-amd64-openstructure-20260124-120050-juju-7f2275-prod-proposed-migration-environment-2-9a4f8f7b-9730-4794-bbe1-c0573dc1c328 --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-openstructure-20260124-120050-juju-7f2275-prod-proposed-migration-environment-2-9a4f8f7b-9730-4794-bbe1-c0573dc1c328 from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 78s autopkgtest [12:02:08]: testbed dpkg architecture: amd64 78s autopkgtest [12:02:08]: testbed apt version: 3.1.13 78s autopkgtest [12:02:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 78s autopkgtest [12:02:08]: testbed release detected to be: None 79s autopkgtest [12:02:09]: updating testbed package index (apt update) 79s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 80s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 80s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 80s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 80s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 80s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 80s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 80s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 80s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 81s Fetched 2806 kB in 1s (2538 kB/s) 81s Reading package lists... 82s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 82s Reading package lists... 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Calculating upgrade... 83s The following packages were automatically installed and are no longer required: 83s python3.13 python3.13-minimal 83s Use 'sudo apt autoremove' to remove them. 83s The following NEW packages will be installed: 83s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 83s The following packages will be upgraded: 83s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 83s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 10.4 MB of archives. 83s After this operation, 25.2 MB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 83s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 83s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 83s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 83s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 83s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 83s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 84s dpkg-preconfigure: unable to re-open stdin: No such file or directory 84s Fetched 10.4 MB in 0s (21.8 MB/s) 84s Selecting previously unselected package libpython3.14-minimal:amd64. 84s (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 ... 124177 files and directories currently installed.) 84s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 84s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 84s Selecting previously unselected package python3.14-minimal. 84s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 84s Unpacking python3.14-minimal (3.14.2-1) ... 84s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 84s Setting up python3.14-minimal (3.14.2-1) ... 84s (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 ... 124519 files and directories currently installed.) 84s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 84s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 85s Setting up python3-minimal (3.14.2-1) ... 85s (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 ... 124519 files and directories currently installed.) 85s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 85s running python pre-rtupdate hooks for python3.14... 85s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 85s Selecting previously unselected package libpython3.14-stdlib:amd64. 85s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 85s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 85s Selecting previously unselected package python3.14. 85s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 85s Unpacking python3.14 (3.14.2-1) ... 85s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 85s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 85s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 85s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 85s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 85s (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 ... 124980 files and directories currently installed.) 85s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 85s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 85s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 85s Setting up python3.14 (3.14.2-1) ... 86s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 86s Setting up python3-gdbm (3.14.2-1) ... 86s Setting up python3 (3.14.2-1) ... 86s running python rtupdate hooks for python3.14... 86s running python post-rtupdate hooks for python3.14... 86s Processing triggers for man-db (2.13.1-1) ... 86s Processing triggers for systemd (259-1ubuntu2) ... 86s autopkgtest [12:02:16]: upgrading testbed (apt dist-upgrade and autopurge) 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 87s The following packages were automatically installed and are no longer required: 87s python3.13 python3.13-minimal 87s Use 'sudo apt autoremove' to remove them. 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Solving dependencies... 87s The following packages will be REMOVED: 87s python3.13* python3.13-minimal* 87s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 87s After this operation, 7860 kB disk space will be freed. 87s (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 ... 124978 files and directories currently installed.) 87s Removing python3.13 (3.13.11-1) ... 87s Removing python3.13-minimal (3.13.11-1) ... 88s Processing triggers for man-db (2.13.1-1) ... 88s Processing triggers for systemd (259-1ubuntu2) ... 88s (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 ... 124951 files and directories currently installed.) 88s Purging configuration files for python3.13-minimal (3.13.11-1) ... 90s autopkgtest [12:02:20]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 91s autopkgtest [12:02:21]: @@@@@@@@@@@@@@@@@@@@ apt-source openstructure 107s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.11.1-1 (dsc) [4885 B] 107s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.11.1-1 (tar) [27.4 MB] 107s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openstructure 2.11.1-1 (diff) [92.3 MB] 107s gpgv: Signature made Wed Oct 15 07:35:46 2025 UTC 107s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 107s gpgv: issuer "merkys@debian.org" 107s gpgv: Can't check signature: No public key 107s dpkg-source: warning: cannot verify inline signature for ./openstructure_2.11.1-1.dsc: no acceptable signature found 109s autopkgtest [12:02:39]: testing package openstructure version 2.11.1-1 117s autopkgtest [12:02:47]: build not needed 127s autopkgtest [12:02:57]: test python: preparing testbed 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Solving dependencies... 128s Some packages could not be installed. This may mean that you have 128s requested an impossible situation or if you are using the unstable 128s distribution that some required packages have not yet been created 128s or been moved out of Incoming. 128s The following information may help to resolve the situation: 128s 128s The following packages have unmet dependencies: 128s satisfy:command-line : Depends: clustalw but it is not going to be installed 128s Depends: dssp but it is not going to be installed 128s Depends: ncbi-blast+ but it is not going to be installed 128s Depends: voronota but it is not going to be installed 128s Depends: libost-base2.11 but it is not going to be installed 128s Depends: libost-bindings2.11 but it is not going to be installed 128s Depends: libost-conop2.11 but it is not going to be installed 128s Depends: libost-db2.11 but it is not going to be installed 128s Depends: libost-geom2.11 but it is not going to be installed 128s Depends: libost-gfx2.11 but it is not going to be installed 128s Depends: libost-gui2.11 but it is not going to be installed 128s Depends: libost-img-alg2.11 but it is not going to be installed 128s Depends: libost-img2.11 but it is not going to be installed 128s Depends: libost-info2.11 but it is not going to be installed 128s Depends: libost-io2.11 but it is not going to be installed 128s Depends: libost-mol-alg2.11 but it is not going to be installed 128s Depends: libost-mol-mm2.11 but it is not going to be installed 128s Depends: libost-mol2.11 but it is not going to be installed 128s Depends: libost-seq-alg2.11 but it is not going to be installed 128s Depends: libost-seq2.11 but it is not going to be installed 128s Depends: openstructure but it is not going to be installed 128s Depends: python3-ost but it is not going to be installed 128s Depends: libost-base-dev but it is not going to be installed 128s Depends: libost-bindings-dev but it is not going to be installed 128s Depends: libost-conop-dev but it is not going to be installed 128s Depends: libost-db-dev but it is not going to be installed 128s Depends: libost-geom-dev but it is not going to be installed 128s Depends: libost-gfx-dev but it is not going to be installed 128s Depends: libost-gui-dev but it is not going to be installed 128s Depends: libost-img-alg-dev but it is not going to be installed 128s Depends: libost-img-dev but it is not going to be installed 128s Depends: libost-info-dev but it is not going to be installed 128s Depends: libost-io-dev but it is not going to be installed 128s Depends: libost-mol-alg-dev but it is not going to be installed 128s Depends: libost-mol-mm-dev but it is not going to be installed 128s Depends: libost-mol-dev but it is not going to be installed 128s Depends: libost-seq-alg-dev but it is not going to be installed 128s Depends: libost-seq-dev but it is not going to be installed 128s E: Unable to satisfy dependencies. Reached two conflicting assignments: 128s 1. python3:amd64=3.13.9-3 is not selected for install 128s 2. python3:amd64=3.13.9-3 is selected as a downgrade because: 128s 1. satisfy:command-line:amd64=1 is selected for install 128s 2. satisfy:command-line:amd64 Depends python3-ost 128s 3. python3-ost:amd64 Depends python3 (< 3.14) 128s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from resolute-proposed 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 128s Solving dependencies... 128s Some packages could not be installed. This may mean that you have 128s requested an impossible situation or if you are using the unstable 128s distribution that some required packages have not yet been created 128s or been moved out of Incoming. 128s The following information may help to resolve the situation: 128s 128s The following packages have unmet dependencies: 128s satisfy:command-line : Depends: clustalw but it is not going to be installed 128s Depends: dssp but it is not going to be installed 128s Depends: ncbi-blast+ but it is not going to be installed 128s Depends: voronota but it is not going to be installed 128s Depends: libost-base2.11 but it is not going to be installed 128s Depends: libost-bindings2.11 but it is not going to be installed 128s Depends: libost-conop2.11 but it is not going to be installed 128s Depends: libost-db2.11 but it is not going to be installed 128s Depends: libost-geom2.11 but it is not going to be installed 128s Depends: libost-gfx2.11 but it is not going to be installed 128s Depends: libost-gui2.11 but it is not going to be installed 128s Depends: libost-img-alg2.11 but it is not going to be installed 128s Depends: libost-img2.11 but it is not going to be installed 128s Depends: libost-info2.11 but it is not going to be installed 128s Depends: libost-io2.11 but it is not going to be installed 128s Depends: libost-mol-alg2.11 but it is not going to be installed 128s Depends: libost-mol-mm2.11 but it is not going to be installed 128s Depends: libost-mol2.11 but it is not going to be installed 128s Depends: libost-seq-alg2.11 but it is not going to be installed 128s Depends: libost-seq2.11 but it is not going to be installed 128s Depends: openstructure but it is not going to be installed 128s Depends: python3-ost but it is not going to be installed 128s Depends: libost-base-dev but it is not going to be installed 128s Depends: libost-bindings-dev but it is not going to be installed 128s Depends: libost-conop-dev but it is not going to be installed 128s Depends: libost-db-dev but it is not going to be installed 128s Depends: libost-geom-dev but it is not going to be installed 128s Depends: libost-gfx-dev but it is not going to be installed 128s Depends: libost-gui-dev but it is not going to be installed 128s Depends: libost-img-alg-dev but it is not going to be installed 128s Depends: libost-img-dev but it is not going to be installed 128s Depends: libost-info-dev but it is not going to be installed 128s Depends: libost-io-dev but it is not going to be installed 128s Depends: libost-mol-alg-dev but it is not going to be installed 128s Depends: libost-mol-mm-dev but it is not going to be installed 128s Depends: libost-mol-dev but it is not going to be installed 128s Depends: libost-seq-alg-dev but it is not going to be installed 128s Depends: libost-seq-dev but it is not going to be installed 128s E: Unable to satisfy dependencies. Reached two conflicting assignments: 128s 1. python3:amd64=3.13.9-3 is not selected for install 128s 2. python3:amd64=3.13.9-3 is selected as a downgrade because: 128s 1. satisfy:command-line:amd64=1 is selected for install 128s 2. satisfy:command-line:amd64 Depends python3-ost 128s 3. python3-ost:amd64 Depends python3 (< 3.14) 128s python FAIL badpkg 128s blame: openstructure 128s badpkg: Test dependencies are unsatisfiable. A common reason is that your testbed is out of date with respect to the archive, and you need to use a current testbed or run apt-get update or use -U. 128s autopkgtest [12:02:58]: @@@@@@@@@@@@@@@@@@@@ summary 128s python FAIL badpkg 128s blame: openstructure 128s badpkg: Test dependencies are unsatisfiable. A common reason is that your testbed is out of date with respect to the archive, and you need to use a current testbed or run apt-get update or use -U.