0s autopkgtest [16:14:46]: starting date and time: 2025-01-03 16:14:46+0000 0s autopkgtest [16:14:46]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:14:46]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.s9ebwqd6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade ont-fast5-api --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-16.secgroup --name adt-plucky-arm64-ont-fast5-api-20250103-161446-juju-7f2275-prod-proposed-migration-environment-20-3dbc307f-f9a5-4c56-8070-32da67780c46 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 142s autopkgtest [16:17:08]: testbed dpkg architecture: arm64 143s autopkgtest [16:17:09]: testbed apt version: 2.9.18 143s autopkgtest [16:17:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 143s autopkgtest [16:17:09]: testbed release detected to be: None 144s autopkgtest [16:17:10]: updating testbed package index (apt update) 144s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 144s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 144s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 145s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 145s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.5 kB] 145s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 145s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 145s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [782 kB] 145s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [98.4 kB] 145s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 145s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [675 kB] 145s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.3 kB] 145s Fetched 1792 kB in 1s (1978 kB/s) 146s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Calculating upgrade... 148s The following packages will be upgraded: 148s base-passwd bash-completion 148s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 267 kB of archives. 148s After this operation, 143 kB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 base-passwd arm64 3.6.6 [53.6 kB] 148s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 bash-completion all 1:2.16.0-1 [214 kB] 149s Preconfiguring packages ... 149s Fetched 267 kB in 0s (567 kB/s) 150s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80060 files and directories currently installed.) 150s Preparing to unpack .../base-passwd_3.6.6_arm64.deb ... 150s Unpacking base-passwd (3.6.6) over (3.6.5) ... 150s Setting up base-passwd (3.6.6) ... 150s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80060 files and directories currently installed.) 150s Preparing to unpack .../bash-completion_1%3a2.16.0-1_all.deb ... 150s Unpacking bash-completion (1:2.16.0-1) over (1:2.14.0-2) ... 150s Setting up bash-completion (1:2.16.0-1) ... 150s Processing triggers for man-db (2.13.0-1) ... 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 153s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 153s autopkgtest [16:17:19]: upgrading testbed (apt dist-upgrade and autopurge) 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 155s Entering ResolveByKeep 155s 156s The following packages were automatically installed and are no longer required: 156s python3.12 python3.12-minimal 156s Use 'sudo apt autoremove' to remove them. 156s The following NEW packages will be installed: 156s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 156s The following packages will be upgraded: 156s libpython3-stdlib python3 python3-minimal 156s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 5992 kB of archives. 156s After this operation, 24.3 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 156s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.13.1-1~exp2 [27.6 kB] 157s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.13.1-1~exp2 [23.9 kB] 157s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 157s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 157s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.13.1-1~exp2 [10.2 kB] 157s Fetched 5992 kB in 1s (7942 kB/s) 157s Selecting previously unselected package libpython3.13-minimal:arm64. 157s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80185 files and directories currently installed.) 157s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_arm64.deb ... 157s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 157s Selecting previously unselected package python3.13-minimal. 157s Preparing to unpack .../python3.13-minimal_3.13.1-2_arm64.deb ... 157s Unpacking python3.13-minimal (3.13.1-2) ... 157s Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... 157s Setting up python3.13-minimal (3.13.1-2) ... 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80505 files and directories currently installed.) 158s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_arm64.deb ... 158s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 158s Setting up python3-minimal (3.13.1-1~exp2) ... 159s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80505 files and directories currently installed.) 159s Preparing to unpack .../python3_3.13.1-1~exp2_arm64.deb ... 159s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 159s Selecting previously unselected package libpython3.13-stdlib:arm64. 159s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_arm64.deb ... 159s Unpacking libpython3.13-stdlib:arm64 (3.13.1-2) ... 159s Selecting previously unselected package python3.13. 159s Preparing to unpack .../python3.13_3.13.1-2_arm64.deb ... 159s Unpacking python3.13 (3.13.1-2) ... 159s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_arm64.deb ... 159s Unpacking libpython3-stdlib:arm64 (3.13.1-1~exp2) over (3.12.8-1) ... 159s Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... 159s Setting up libpython3-stdlib:arm64 (3.13.1-1~exp2) ... 159s Setting up python3.13 (3.13.1-2) ... 160s Setting up python3 (3.13.1-1~exp2) ... 160s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 160s for fn in glob1(directory, "%s.*" % fname): 161s Processing triggers for man-db (2.13.0-1) ... 161s Processing triggers for systemd (257-2ubuntu1) ... 161s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 163s The following packages will be REMOVED: 163s python3.12* python3.12-minimal* 163s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 163s After this operation, 8710 kB disk space will be freed. 163s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80922 files and directories currently installed.) 163s Removing python3.12 (3.12.8-3) ... 163s Removing python3.12-minimal (3.12.8-3) ... 164s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 164s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 164s Processing triggers for man-db (2.13.0-1) ... 164s Processing triggers for systemd (257-2ubuntu1) ... 165s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80894 files and directories currently installed.) 165s Purging configuration files for python3.12-minimal (3.12.8-3) ... 167s autopkgtest [16:17:33]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 167s autopkgtest [16:17:33]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 169s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4build1 (dsc) [2235 B] 169s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4build1 (tar) [1384 kB] 169s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4build1 (diff) [4660 B] 169s gpgv: Signature made Fri Nov 15 13:41:08 2024 UTC 169s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 169s gpgv: Can't check signature: No public key 169s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.1+dfsg-4build1.dsc: no acceptable signature found 170s autopkgtest [16:17:36]: testing package ont-fast5-api version 4.1.1+dfsg-4build1 170s autopkgtest [16:17:36]: build not needed 171s autopkgtest [16:17:37]: test run-unit-test: preparing testbed 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 172s The following NEW packages will be installed: 172s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 172s liblzf1 libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api 172s python3-all python3-h5py python3-h5py-serial python3-numpy python3-packaging 172s python3-progressbar python3.12 python3.12-minimal 173s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 12.9 MB of archives. 173s After this operation, 59.7 MB of additional disk space will be used. 173s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-minimal arm64 3.12.8-3 [2236 kB] 173s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12 arm64 3.12.8-3 [667 kB] 173s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 173s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 173s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 173s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 173s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-5ubuntu1 [1210 kB] 173s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-5ubuntu1 [56.9 kB] 173s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 173s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 173s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin0t64 arm64 1.0.2-3.1build1 [18.2 kB] 173s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin-dev arm64 1.0.2-3.1build1 [14.4 kB] 173s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 173s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 173s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 173s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 173s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-progressbar all 2.5-4 [11.0 kB] 173s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 ont-fast5-api arm64 4.1.1+dfsg-4build1 [47.8 kB] 173s Get:19 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.13.1-1~exp2 [894 B] 174s Fetched 12.9 MB in 1s (14.0 MB/s) 174s Selecting previously unselected package python3.12-minimal. 174s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80894 files and directories currently installed.) 174s Preparing to unpack .../00-python3.12-minimal_3.12.8-3_arm64.deb ... 174s Unpacking python3.12-minimal (3.12.8-3) ... 174s Selecting previously unselected package python3.12. 174s Preparing to unpack .../01-python3.12_3.12.8-3_arm64.deb ... 174s Unpacking python3.12 (3.12.8-3) ... 174s Selecting previously unselected package libaec0:arm64. 174s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 174s Unpacking libaec0:arm64 (1.1.3-1) ... 174s Selecting previously unselected package libblas3:arm64. 174s Preparing to unpack .../03-libblas3_3.12.0-4_arm64.deb ... 174s Unpacking libblas3:arm64 (3.12.0-4) ... 174s Selecting previously unselected package libgfortran5:arm64. 174s Preparing to unpack .../04-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 174s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 174s Selecting previously unselected package libsz2:arm64. 174s Preparing to unpack .../05-libsz2_1.1.3-1_arm64.deb ... 174s Unpacking libsz2:arm64 (1.1.3-1) ... 174s Selecting previously unselected package libhdf5-103-1t64:arm64. 174s Preparing to unpack .../06-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_arm64.deb ... 174s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 174s Selecting previously unselected package libhdf5-hl-100t64:arm64. 174s Preparing to unpack .../07-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_arm64.deb ... 174s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 174s Selecting previously unselected package liblapack3:arm64. 174s Preparing to unpack .../08-liblapack3_3.12.0-4_arm64.deb ... 174s Unpacking liblapack3:arm64 (3.12.0-4) ... 174s Selecting previously unselected package liblzf1:arm64. 174s Preparing to unpack .../09-liblzf1_3.6-4_arm64.deb ... 174s Unpacking liblzf1:arm64 (3.6-4) ... 174s Selecting previously unselected package libvbz-hdf-plugin0t64:arm64. 174s Preparing to unpack .../10-libvbz-hdf-plugin0t64_1.0.2-3.1build1_arm64.deb ... 174s Unpacking libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 174s Selecting previously unselected package libvbz-hdf-plugin-dev:arm64. 174s Preparing to unpack .../11-libvbz-hdf-plugin-dev_1.0.2-3.1build1_arm64.deb ... 174s Unpacking libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 174s Selecting previously unselected package python3-numpy. 174s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 174s Unpacking python3-numpy (1:1.26.4+ds-12) ... 175s Selecting previously unselected package python3-h5py-serial. 175s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 175s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 175s Selecting previously unselected package python3-h5py. 175s Preparing to unpack .../14-python3-h5py_3.11.0-8ubuntu3_all.deb ... 175s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 175s Selecting previously unselected package python3-packaging. 175s Preparing to unpack .../15-python3-packaging_24.2-1_all.deb ... 175s Unpacking python3-packaging (24.2-1) ... 175s Selecting previously unselected package python3-progressbar. 175s Preparing to unpack .../16-python3-progressbar_2.5-4_all.deb ... 175s Unpacking python3-progressbar (2.5-4) ... 175s Selecting previously unselected package ont-fast5-api. 175s Preparing to unpack .../17-ont-fast5-api_4.1.1+dfsg-4build1_arm64.deb ... 175s Unpacking ont-fast5-api (4.1.1+dfsg-4build1) ... 175s Selecting previously unselected package python3-all. 175s Preparing to unpack .../18-python3-all_3.13.1-1~exp2_arm64.deb ... 175s Unpacking python3-all (3.13.1-1~exp2) ... 175s Setting up python3.12-minimal (3.12.8-3) ... 176s Setting up python3.12 (3.12.8-3) ... 178s Setting up python3-all (3.13.1-1~exp2) ... 178s Setting up libaec0:arm64 (1.1.3-1) ... 178s Setting up libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 178s Setting up python3-progressbar (2.5-4) ... 178s Setting up libblas3:arm64 (3.12.0-4) ... 178s 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 178s Setting up python3-packaging (24.2-1) ... 178s Setting up liblzf1:arm64 (3.6-4) ... 178s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 178s Setting up libsz2:arm64 (1.1.3-1) ... 178s Setting up liblapack3:arm64 (3.12.0-4) ... 178s 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 178s Setting up libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 178s Setting up python3-numpy (1:1.26.4+ds-12) ... 183s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 183s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 183s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 183s Setting up python3-h5py (3.11.0-8ubuntu3) ... 183s Setting up ont-fast5-api (4.1.1+dfsg-4build1) ... 184s Processing triggers for systemd (257-2ubuntu1) ... 184s Processing triggers for man-db (2.13.0-1) ... 184s Processing triggers for libc-bin (2.40-4ubuntu1) ... 185s autopkgtest [16:17:51]: test run-unit-test: [----------------------- 186s test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ... ok 186s test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ... ok 186s test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ... ok 186s test_check_multi_read (test.test_check_compression.TestCheckCompression.test_check_multi_read) ... ok 186s test_check_read_compression_multi_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_multi_read) ... ok 186s test_check_read_compression_single_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_single_read) ... ok 186s test_check_read_compression_vbz (test.test_check_compression.TestCheckCompression.test_check_read_compression_vbz) ... ok 186s test_check_single_read_folder (test.test_check_compression.TestCheckCompression.test_check_single_read_folder) ... ok 186s test_multi_to_multi (test.test_compress_fast5.TestSanitise.test_multi_to_multi) ... ok 186s test_single_to_multi (test.test_compress_fast5.TestSanitise.test_single_to_multi) ... ok 186s test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert.test_add_read_from_multi) ... ok 186s test_compress_in_place (test.test_compress_fast5.TestVbzConvert.test_compress_in_place) ... skipped 'Permission Denied - to open folder' 186s test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert.test_compress_read_from_single) ... ok 186s test_conversion_script_multi (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi) ... skipped 'Permission Denied - to open folder' 186s test_conversion_script_multi_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi_retains_end_reason_enumeration) 186s Test that given a collection of multi read fast5 files that undergo compression ... ok 186s test_conversion_script_single (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single) ... skipped 'Permission Denied - to open folder' 186s test_conversion_script_single_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single_retains_end_reason_enumeration) 186s Test that given a collection of single read fast5 files that undergo compression ... ok 186s test_read_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_read_vbz_using_api) ... ok 186s test_write_vbz_directly (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_directly) ... skipped 'Tries to create dataset - permission denied' 186s test_write_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api) ... ok 186s test_write_vbz_using_api_single_read (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api_single_read) ... ok 186s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ok 186s test__clean (test.test_data_sanitisation.TestDataSanitisation.test__clean) ... ok 186s test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ... ok 186s test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ... ok 186s test_real_example_file (test.test_data_sanitisation.TestDataSanitisation.test_real_example_file) ... ok 186s test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ... ok 186s test_demux_1t (test.test_demux_fast5.TestDemuxFast5.test_demux_1t) ... ok 187s test_demux_8t (test.test_demux_fast5.TestDemuxFast5.test_demux_8t) ... ok 187s test_parse_summary (test.test_demux_fast5.TestDemuxFast5.test_parse_summary) ... ok 187s test_001_read_events (test.test_event_detection_tools.TestEventDetectionTools.test_001_read_events) ... ok 187s test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ... ok 187s test_yield_fast5_files_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_dir) ... ok 187s test_yield_fast5_files_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_fast5_file) ... ok 187s test_yield_fast5_reads_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_dir) ... ok 187s test_yield_fast5_reads_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_fast5_file) ... ok 187s test_yield_fast5_reads_set_versus_list_equality (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_set_versus_list_equality) ... ok 187s test_yield_fast5_reads_type_error (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_type_error) ... ok 187s test_yield_fast5_reads_with_empty_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_empty_set) ... ok 187s test_yield_fast5_reads_with_garbage_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_garbage_set) ... ok 187s test_yield_fast5_reads_with_list (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_list) ... ok 187s test_yield_fast5_reads_with_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_set) ... ok 187s test_add_read_to_multi (test.test_fast5_converter.TestFast5Converter.test_add_read_to_multi) ... ok 187s test_multi_to_single (test.test_fast5_converter.TestFast5Converter.test_multi_to_single) ... ok 187s test_multi_to_single_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_multi_to_single_incorrect_types) ... ok 187s test_single_to_multi (test.test_fast5_converter.TestFast5Converter.test_single_to_multi) ... skipped 'Permission Denied - to open folder' 187s test_single_to_multi_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_single_to_multi_incorrect_types) ... ok 187s test_001_get_latest_analysis (test.test_fast5_file.TestFast5File.test_001_get_latest_analysis) ... ok 187s test_002_add_analysis_group (test.test_fast5_file.TestFast5File.test_002_add_analysis_group) ... ok 187s test_002_read_summary_data (test.test_fast5_file.TestFast5File.test_002_read_summary_data) ... ok 187s test_003_add_analysis_subgroup (test.test_fast5_file.TestFast5File.test_003_add_analysis_subgroup) ... ok 187s test_010_v0_6_single (test.test_fast5_file.TestFast5File.test_010_v0_6_single) ... ok 187s test_011_v0_6_raw (test.test_fast5_file.TestFast5File.test_011_v0_6_raw) ... ok 187s test_012_v1_0_single (test.test_fast5_file.TestFast5File.test_012_v1_0_single) ... ok 187s test_fast5_add_analysis_dataset (test.test_fast5_file.TestFast5File.test_fast5_add_analysis_dataset) ... ok 187s test_fast5_add_and_get_chain (test.test_fast5_file.TestFast5File.test_fast5_add_and_get_chain) ... ok 187s test_fast5_add_group (test.test_fast5_file.TestFast5File.test_fast5_add_group) ... ok 187s test_fast5_set_analysis_config (test.test_fast5_file.TestFast5File.test_fast5_set_analysis_config) ... ok 187s test_correct_type (test.test_fast5_interface.TestFast5Interface.test_correct_type) ... ok 187s test_extract_selected_reads (test.test_fast5_subset.TestFast5Subset.test_extract_selected_reads) ... ok 187s test_read_generator (test.test_fast5_subset.TestFast5Subset.test_read_generator) ... ok 187s test_selector_args_generator (test.test_fast5_subset.TestFast5Subset.test_selector_args_generator) ... ok 187s test_subset_from_multi (test.test_fast5_subset.TestFast5Subset.test_subset_from_multi) ... ok 187s test_subset_from_single (test.test_fast5_subset.TestFast5Subset.test_subset_from_single) ... ok 187s test_create_read (test.test_hardlink_metadata.TestHardlinkMetaData.test_create_read) ... ok 188s test_hardlink_multi_compression (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_multi_compression) ... ok 188s test_hardlink_single_to_multi (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_single_to_multi) ... ok 188s test_hardlink_subset (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset) ... ok 188s test_hardlink_subset_single_reads (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset_single_reads) ... ok 188s test_add_analysis (test.test_multi_fast5.TestMultiFast5.test_add_analysis) ... ok 188s test_channel_info (test.test_multi_fast5.TestMultiFast5.test_channel_info) ... ok 188s test_raw_data (test.test_multi_fast5.TestMultiFast5.test_raw_data) ... ok 188s test_read_interface (test.test_multi_fast5.TestMultiFast5.test_read_interface) ... ok 188s test_tracking_id (test.test_multi_fast5.TestMultiFast5.test_tracking_id) ... ok 188s test_001_raw_only (test.test_segmentation_tools.TestSegmentationTools.test_001_raw_only) ... ok 188s test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ok 188s 188s ---------------------------------------------------------------------- 188s Ran 76 tests in 1.881s 188s 188s OK (skipped=5) 188s test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ... ok 188s test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ... ok 188s test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ... ok 188s test_check_multi_read (test.test_check_compression.TestCheckCompression.test_check_multi_read) ... ok 188s test_check_read_compression_multi_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_multi_read) ... ok 188s test_check_read_compression_single_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_single_read) ... ok 188s test_check_read_compression_vbz (test.test_check_compression.TestCheckCompression.test_check_read_compression_vbz) ... ok 188s test_check_single_read_folder (test.test_check_compression.TestCheckCompression.test_check_single_read_folder) ... ok 188s test_multi_to_multi (test.test_compress_fast5.TestSanitise.test_multi_to_multi) ... ok 188s test_single_to_multi (test.test_compress_fast5.TestSanitise.test_single_to_multi) ... ok 188s test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert.test_add_read_from_multi) ... ok 188s test_compress_in_place (test.test_compress_fast5.TestVbzConvert.test_compress_in_place) ... skipped 'Permission Denied - to open folder' 188s test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert.test_compress_read_from_single) ... ok 188s test_conversion_script_multi (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi) ... skipped 'Permission Denied - to open folder' 188s test_conversion_script_multi_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi_retains_end_reason_enumeration) 189s Test that given a collection of multi read fast5 files that undergo compression ... ok 189s test_conversion_script_single (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single) ... skipped 'Permission Denied - to open folder' 189s test_conversion_script_single_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single_retains_end_reason_enumeration) 189s Test that given a collection of single read fast5 files that undergo compression ... ok 189s test_read_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_read_vbz_using_api) ... ok 189s test_write_vbz_directly (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_directly) ... skipped 'Tries to create dataset - permission denied' 189s test_write_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api) ... ok 189s test_write_vbz_using_api_single_read (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api_single_read) ... ok 189s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ok 189s test__clean (test.test_data_sanitisation.TestDataSanitisation.test__clean) ... ok 189s test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ... ok 189s test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ... ok 189s test_real_example_file (test.test_data_sanitisation.TestDataSanitisation.test_real_example_file) ... ok 189s test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ... ok 189s test_demux_1t (test.test_demux_fast5.TestDemuxFast5.test_demux_1t) ... ok 190s test_demux_8t (test.test_demux_fast5.TestDemuxFast5.test_demux_8t) ... ok 190s test_parse_summary (test.test_demux_fast5.TestDemuxFast5.test_parse_summary) ... ok 190s test_001_read_events (test.test_event_detection_tools.TestEventDetectionTools.test_001_read_events) ... ok 190s test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ... ok 190s test_yield_fast5_files_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_dir) ... ok 190s test_yield_fast5_files_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_fast5_file) ... ok 190s test_yield_fast5_reads_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_dir) ... ok 190s test_yield_fast5_reads_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_fast5_file) ... ok 190s test_yield_fast5_reads_set_versus_list_equality (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_set_versus_list_equality) ... ok 190s test_yield_fast5_reads_type_error (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_type_error) ... ok 190s test_yield_fast5_reads_with_empty_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_empty_set) ... ok 190s test_yield_fast5_reads_with_garbage_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_garbage_set) ... ok 190s test_yield_fast5_reads_with_list (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_list) ... ok 190s test_yield_fast5_reads_with_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_set) ... ok 190s test_add_read_to_multi (test.test_fast5_converter.TestFast5Converter.test_add_read_to_multi) ... ok 190s test_multi_to_single (test.test_fast5_converter.TestFast5Converter.test_multi_to_single) ... ok 190s test_multi_to_single_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_multi_to_single_incorrect_types) ... ok 190s test_single_to_multi (test.test_fast5_converter.TestFast5Converter.test_single_to_multi) ... skipped 'Permission Denied - to open folder' 190s test_single_to_multi_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_single_to_multi_incorrect_types) ... ok 190s test_001_get_latest_analysis (test.test_fast5_file.TestFast5File.test_001_get_latest_analysis) ... ok 190s test_002_add_analysis_group (test.test_fast5_file.TestFast5File.test_002_add_analysis_group) ... ok 190s test_002_read_summary_data (test.test_fast5_file.TestFast5File.test_002_read_summary_data) ... ok 190s test_003_add_analysis_subgroup (test.test_fast5_file.TestFast5File.test_003_add_analysis_subgroup) ... ok 190s test_010_v0_6_single (test.test_fast5_file.TestFast5File.test_010_v0_6_single) ... ok 190s test_011_v0_6_raw (test.test_fast5_file.TestFast5File.test_011_v0_6_raw) ... ok 190s test_012_v1_0_single (test.test_fast5_file.TestFast5File.test_012_v1_0_single) ... ok 190s test_fast5_add_analysis_dataset (test.test_fast5_file.TestFast5File.test_fast5_add_analysis_dataset) ... ok 190s test_fast5_add_and_get_chain (test.test_fast5_file.TestFast5File.test_fast5_add_and_get_chain) ... ok 190s test_fast5_add_group (test.test_fast5_file.TestFast5File.test_fast5_add_group) ... ok 190s test_fast5_set_analysis_config (test.test_fast5_file.TestFast5File.test_fast5_set_analysis_config) ... ok 190s test_correct_type (test.test_fast5_interface.TestFast5Interface.test_correct_type) ... ok 190s test_extract_selected_reads (test.test_fast5_subset.TestFast5Subset.test_extract_selected_reads) ... ok 190s test_read_generator (test.test_fast5_subset.TestFast5Subset.test_read_generator) ... ok 190s test_selector_args_generator (test.test_fast5_subset.TestFast5Subset.test_selector_args_generator) ... ok 190s test_subset_from_multi (test.test_fast5_subset.TestFast5Subset.test_subset_from_multi) ... ok 190s test_subset_from_single (test.test_fast5_subset.TestFast5Subset.test_subset_from_single) ... ok 190s test_create_read (test.test_hardlink_metadata.TestHardlinkMetaData.test_create_read) ... ok 190s test_hardlink_multi_compression (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_multi_compression) ... ok 190s test_hardlink_single_to_multi (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_single_to_multi) ... ok 190s test_hardlink_subset (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset) ... ok 190s test_hardlink_subset_single_reads (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset_single_reads) ... ok 190s test_add_analysis (test.test_multi_fast5.TestMultiFast5.test_add_analysis) ... ok 190s test_channel_info (test.test_multi_fast5.TestMultiFast5.test_channel_info) ... ok 190s test_raw_data (test.test_multi_fast5.TestMultiFast5.test_raw_data) ... ok 190s test_read_interface (test.test_multi_fast5.TestMultiFast5.test_read_interface) ... ok 190s test_tracking_id (test.test_multi_fast5.TestMultiFast5.test_tracking_id) ... ok 190s test_001_raw_only (test.test_segmentation_tools.TestSegmentationTools.test_001_raw_only) ... ok 190s test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ok 190s 190s ---------------------------------------------------------------------- 190s Ran 76 tests in 1.834s 190s 190s OK (skipped=5) 191s autopkgtest [16:17:57]: test run-unit-test: -----------------------] 191s autopkgtest [16:17:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 191s run-unit-test PASS 191s autopkgtest [16:17:57]: @@@@@@@@@@@@@@@@@@@@ summary 191s run-unit-test PASS 208s nova [W] Using flock in prodstack6-arm64 208s Creating nova instance adt-plucky-arm64-ont-fast5-api-20250103-161446-juju-7f2275-prod-proposed-migration-environment-20-3dbc307f-f9a5-4c56-8070-32da67780c46 from image adt/ubuntu-plucky-arm64-server-20250102.img (UUID 4cb073f4-4206-4362-b576-2406cb25ddd8)... 208s nova [W] Timed out waiting for 2cb49bcc-6d52-426c-95a4-8fc577e9a8bb to get deleted.