0s autopkgtest [13:53:18]: starting date and time: 2025-03-15 13:53:18+0000 0s autopkgtest [13:53:18]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:53:18]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._mc4asi2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade ont-fast5-api --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-29.secgroup --name adt-plucky-arm64-ont-fast5-api-20250315-135318-juju-7f2275-prod-proposed-migration-environment-20-fc2c2bdf-5462-4029-84ff-b0995811fc0d --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/ 174s autopkgtest [13:56:12]: testbed dpkg architecture: arm64 174s autopkgtest [13:56:12]: testbed apt version: 2.9.33 174s autopkgtest [13:56:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 174s autopkgtest [13:56:12]: testbed release detected to be: None 175s autopkgtest [13:56:13]: updating testbed package index (apt update) 176s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 176s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 176s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 176s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 176s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 176s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 177s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 177s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 177s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 177s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 177s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 177s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 177s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 177s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 178s Fetched 1094 kB in 2s (525 kB/s) 179s Reading package lists... 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Calculating upgrade... 180s Calculating upgrade... 181s The following packages will be upgraded: 181s python3-jinja2 strace 181s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 608 kB of archives. 181s After this operation, 11.3 kB of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 181s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 182s Fetched 608 kB in 1s (660 kB/s) 182s (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 ... 117701 files and directories currently installed.) 182s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 182s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 182s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 182s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 183s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 183s Setting up strace (6.13+ds-1ubuntu1) ... 183s Processing triggers for man-db (2.13.0-1) ... 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 184s Solving dependencies... 184s The following packages will be REMOVED: 184s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 184s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 184s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 184s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 185s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 185s After this operation, 267 MB disk space will be freed. 185s (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 ... 117701 files and directories currently installed.) 185s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 185s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 185s Removing libpython3.12t64:arm64 (3.12.9-1) ... 185s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 185s Removing libnsl2:arm64 (1.3.0-3build3) ... 185s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 185s Removing libunwind8:arm64 (1.6.2-3.1) ... 185s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 186s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 187s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 187s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 187s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 187s /etc/kernel/postrm.d/initramfs-tools: 187s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 187s /etc/kernel/postrm.d/zz-flash-kernel: 187s flash-kernel: Kernel 6.11.0-8-generic has been removed. 187s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 188s /etc/kernel/postrm.d/zz-update-grub: 188s Sourcing file `/etc/default/grub' 188s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 188s Generating grub configuration file ... 188s Found linux image: /boot/vmlinuz-6.14.0-10-generic 188s Found initrd image: /boot/initrd.img-6.14.0-10-generic 188s Warning: os-prober will not be executed to detect other bootable partitions. 188s Systems on them will not be added to the GRUB boot configuration. 188s Check GRUB_DISABLE_OS_PROBER documentation entry. 188s Adding boot menu entry for UEFI Firmware Settings ... 188s done 188s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 189s Processing triggers for libc-bin (2.41-1ubuntu1) ... 189s (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 ... 81650 files and directories currently installed.) 189s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 189s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 189s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 189s autopkgtest [13:56:27]: upgrading testbed (apt dist-upgrade and autopurge) 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s Entering ResolveByKeep 191s 191s Calculating upgrade... 192s The following packages will be upgraded: 192s libc-bin libc-dev-bin libc6 libc6-dev locales 192s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 9530 kB of archives. 192s After this operation, 0 B of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 198s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 199s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 204s Preconfiguring packages ... 204s Fetched 9530 kB in 12s (803 kB/s) 204s (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 ... 81647 files and directories currently installed.) 204s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 204s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 204s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 205s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up libc6:arm64 (2.41-1ubuntu2) ... 205s (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 ... 81647 files and directories currently installed.) 205s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 205s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up libc-bin (2.41-1ubuntu2) ... 205s (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 ... 81647 files and directories currently installed.) 205s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 205s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 205s Setting up locales (2.41-1ubuntu2) ... 206s Generating locales (this might take a while)... 208s en_US.UTF-8... done 208s Generation complete. 208s Setting up libc-dev-bin (2.41-1ubuntu2) ... 208s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 208s Processing triggers for man-db (2.13.0-1) ... 209s Processing triggers for systemd (257.3-1ubuntu3) ... 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 211s Solving dependencies... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 212s autopkgtest [13:56:50]: rebooting testbed after setup commands that affected boot 237s autopkgtest [13:57:15]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 239s autopkgtest [13:57:17]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 243s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.3+dfsg-1build1 (dsc) [2245 B] 243s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.3+dfsg-1build1 (tar) [1387 kB] 243s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.3+dfsg-1build1 (diff) [4724 B] 243s gpgv: Signature made Tue Mar 4 15:09:26 2025 UTC 243s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 243s gpgv: Can't check signature: No public key 243s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.3+dfsg-1build1.dsc: no acceptable signature found 243s autopkgtest [13:57:21]: testing package ont-fast5-api version 4.1.3+dfsg-1build1 244s autopkgtest [13:57:22]: build not needed 245s autopkgtest [13:57:23]: test run-unit-test: preparing testbed 245s Reading package lists... 245s Building dependency tree... 245s Reading state information... 245s Starting pkgProblemResolver with broken count: 0 246s Starting 2 pkgProblemResolver with broken count: 0 246s Done 246s The following NEW packages will be installed: 246s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 liblzf1 246s libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api python3-all 246s python3-h5py python3-h5py-serial python3-numpy python3-numpy-dev 246s python3-packaging python3-progressbar 246s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 246s Need to get 9741 kB of archives. 246s After this operation, 41.1 MB of additional disk space will be used. 246s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 248s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 250s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 255s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 255s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 255s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB] 257s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB] 257s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 257s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin0t64 arm64 1.0.2-3.1build1 [18.2 kB] 257s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin-dev arm64 1.0.2-3.1build1 [14.4 kB] 257s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.13.0-1 [1126 kB] 258s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.13.0-1 [7978 B] 258s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 258s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-progressbar all 2.5-4 [11.0 kB] 258s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 ont-fast5-api arm64 4.1.3+dfsg-1build1 [48.0 kB] 258s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 259s Fetched 9741 kB in 12s (819 kB/s) 259s Selecting previously unselected package python3-numpy-dev:arm64. 259s (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 ... 81647 files and directories currently installed.) 259s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 259s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 259s Selecting previously unselected package libblas3:arm64. 259s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 259s Unpacking libblas3:arm64 (3.12.1-2) ... 259s Selecting previously unselected package libgfortran5:arm64. 259s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 259s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 259s Selecting previously unselected package liblapack3:arm64. 259s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 259s Unpacking liblapack3:arm64 (3.12.1-2) ... 259s Selecting previously unselected package python3-numpy. 259s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 259s Unpacking python3-numpy (1:2.2.3+ds-5) ... 259s Selecting previously unselected package libaec0:arm64. 259s Preparing to unpack .../05-libaec0_1.1.3-1_arm64.deb ... 259s Unpacking libaec0:arm64 (1.1.3-1) ... 259s Selecting previously unselected package libsz2:arm64. 259s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 259s Unpacking libsz2:arm64 (1.1.3-1) ... 259s Selecting previously unselected package libhdf5-310:arm64. 259s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_arm64.deb ... 259s Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... 260s Selecting previously unselected package libhdf5-hl-310:arm64. 260s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... 260s Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 260s Selecting previously unselected package liblzf1:arm64. 260s Preparing to unpack .../09-liblzf1_3.6-4_arm64.deb ... 260s Unpacking liblzf1:arm64 (3.6-4) ... 260s Selecting previously unselected package libvbz-hdf-plugin0t64:arm64. 260s Preparing to unpack .../10-libvbz-hdf-plugin0t64_1.0.2-3.1build1_arm64.deb ... 260s Unpacking libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 260s Selecting previously unselected package libvbz-hdf-plugin-dev:arm64. 260s Preparing to unpack .../11-libvbz-hdf-plugin-dev_1.0.2-3.1build1_arm64.deb ... 260s Unpacking libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 260s Selecting previously unselected package python3-h5py-serial. 260s Preparing to unpack .../12-python3-h5py-serial_3.13.0-1_arm64.deb ... 260s Unpacking python3-h5py-serial (3.13.0-1) ... 260s Selecting previously unselected package python3-h5py. 260s Preparing to unpack .../13-python3-h5py_3.13.0-1_all.deb ... 260s Unpacking python3-h5py (3.13.0-1) ... 260s Selecting previously unselected package python3-packaging. 260s Preparing to unpack .../14-python3-packaging_24.2-1_all.deb ... 260s Unpacking python3-packaging (24.2-1) ... 260s Selecting previously unselected package python3-progressbar. 260s Preparing to unpack .../15-python3-progressbar_2.5-4_all.deb ... 260s Unpacking python3-progressbar (2.5-4) ... 260s Selecting previously unselected package ont-fast5-api. 260s Preparing to unpack .../16-ont-fast5-api_4.1.3+dfsg-1build1_arm64.deb ... 260s Unpacking ont-fast5-api (4.1.3+dfsg-1build1) ... 260s Selecting previously unselected package python3-all. 260s Preparing to unpack .../17-python3-all_3.13.2-2_arm64.deb ... 260s Unpacking python3-all (3.13.2-2) ... 260s Setting up python3-all (3.13.2-2) ... 260s Setting up libaec0:arm64 (1.1.3-1) ... 260s Setting up libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 260s Setting up python3-progressbar (2.5-4) ... 260s Setting up libblas3:arm64 (3.12.1-2) ... 260s 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 260s Setting up python3-packaging (24.2-1) ... 260s Setting up liblzf1:arm64 (3.6-4) ... 260s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 260s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 260s Setting up libsz2:arm64 (1.1.3-1) ... 260s Setting up liblapack3:arm64 (3.12.1-2) ... 260s 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 260s Setting up libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 260s Setting up python3-numpy (1:2.2.3+ds-5) ... 262s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... 262s Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... 262s Setting up python3-h5py-serial (3.13.0-1) ... 262s Setting up python3-h5py (3.13.0-1) ... 263s Setting up ont-fast5-api (4.1.3+dfsg-1build1) ... 263s Processing triggers for man-db (2.13.0-1) ... 263s Processing triggers for libc-bin (2.41-1ubuntu2) ... 265s autopkgtest [13:57:43]: test run-unit-test: [----------------------- 265s test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ... ok 265s test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ... ok 265s test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ... ok 265s test_check_multi_read (test.test_check_compression.TestCheckCompression.test_check_multi_read) ... ok 265s test_check_read_compression_multi_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_multi_read) ... ok 265s test_check_read_compression_single_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_single_read) ... ok 265s test_check_read_compression_vbz (test.test_check_compression.TestCheckCompression.test_check_read_compression_vbz) ... ok 265s test_check_single_read_folder (test.test_check_compression.TestCheckCompression.test_check_single_read_folder) ... ok 265s test_multi_to_multi (test.test_compress_fast5.TestSanitise.test_multi_to_multi) ... ok 265s test_single_to_multi (test.test_compress_fast5.TestSanitise.test_single_to_multi) ... ok 265s test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert.test_add_read_from_multi) ... ok 265s test_compress_in_place (test.test_compress_fast5.TestVbzConvert.test_compress_in_place) ... skipped 'Permission Denied - to open folder' 265s test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert.test_compress_read_from_single) ... ok 265s test_conversion_script_multi (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi) ... skipped 'Permission Denied - to open folder' 265s test_conversion_script_multi_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi_retains_end_reason_enumeration) 265s Test that given a collection of multi read fast5 files that undergo compression ... ok 265s test_conversion_script_single (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single) ... skipped 'Permission Denied - to open folder' 265s test_conversion_script_single_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single_retains_end_reason_enumeration) 266s Test that given a collection of single read fast5 files that undergo compression ... ok 266s test_read_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_read_vbz_using_api) ... ok 266s test_write_vbz_directly (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_directly) ... skipped 'Tries to create dataset - permission denied' 266s test_write_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api) ... ok 266s test_write_vbz_using_api_single_read (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api_single_read) ... ok 266s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ok 266s test__clean (test.test_data_sanitisation.TestDataSanitisation.test__clean) ... ok 266s test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ... ok 266s test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ... ok 266s test_real_example_file (test.test_data_sanitisation.TestDataSanitisation.test_real_example_file) ... ok 266s test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ... ok 266s test_demux_1t (test.test_demux_fast5.TestDemuxFast5.test_demux_1t) ... ok 267s test_demux_8t (test.test_demux_fast5.TestDemuxFast5.test_demux_8t) ... ok 267s test_parse_summary (test.test_demux_fast5.TestDemuxFast5.test_parse_summary) ... ok 267s test_001_read_events (test.test_event_detection_tools.TestEventDetectionTools.test_001_read_events) ... ok 267s test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ... ok 267s test_yield_fast5_files_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_dir) ... ok 267s test_yield_fast5_files_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_fast5_file) ... ok 267s test_yield_fast5_reads_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_dir) ... ok 267s test_yield_fast5_reads_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_fast5_file) ... ok 267s test_yield_fast5_reads_set_versus_list_equality (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_set_versus_list_equality) ... ok 267s test_yield_fast5_reads_type_error (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_type_error) ... ok 267s test_yield_fast5_reads_with_empty_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_empty_set) ... ok 267s test_yield_fast5_reads_with_garbage_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_garbage_set) ... ok 267s test_yield_fast5_reads_with_list (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_list) ... ok 267s test_yield_fast5_reads_with_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_set) ... ok 267s test_add_read_to_multi (test.test_fast5_converter.TestFast5Converter.test_add_read_to_multi) ... ok 267s test_multi_to_single (test.test_fast5_converter.TestFast5Converter.test_multi_to_single) ... ok 267s test_multi_to_single_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_multi_to_single_incorrect_types) ... ok 267s test_single_to_multi (test.test_fast5_converter.TestFast5Converter.test_single_to_multi) ... skipped 'Permission Denied - to open folder' 267s test_single_to_multi_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_single_to_multi_incorrect_types) ... ok 267s test_001_get_latest_analysis (test.test_fast5_file.TestFast5File.test_001_get_latest_analysis) ... ok 267s test_002_add_analysis_group (test.test_fast5_file.TestFast5File.test_002_add_analysis_group) ... ok 267s test_002_read_summary_data (test.test_fast5_file.TestFast5File.test_002_read_summary_data) ... ok 267s test_003_add_analysis_subgroup (test.test_fast5_file.TestFast5File.test_003_add_analysis_subgroup) ... ok 267s test_010_v0_6_single (test.test_fast5_file.TestFast5File.test_010_v0_6_single) ... ok 267s test_011_v0_6_raw (test.test_fast5_file.TestFast5File.test_011_v0_6_raw) ... ok 267s test_012_v1_0_single (test.test_fast5_file.TestFast5File.test_012_v1_0_single) ... ok 267s test_fast5_add_analysis_dataset (test.test_fast5_file.TestFast5File.test_fast5_add_analysis_dataset) ... ok 267s test_fast5_add_and_get_chain (test.test_fast5_file.TestFast5File.test_fast5_add_and_get_chain) ... ok 267s test_fast5_add_group (test.test_fast5_file.TestFast5File.test_fast5_add_group) ... ok 267s test_fast5_set_analysis_config (test.test_fast5_file.TestFast5File.test_fast5_set_analysis_config) ... ok 267s test_correct_type (test.test_fast5_interface.TestFast5Interface.test_correct_type) ... ok 267s test_extract_selected_reads (test.test_fast5_subset.TestFast5Subset.test_extract_selected_reads) ... ok 267s test_read_generator (test.test_fast5_subset.TestFast5Subset.test_read_generator) ... ok 267s test_selector_args_generator (test.test_fast5_subset.TestFast5Subset.test_selector_args_generator) ... ok 267s test_subset_from_multi (test.test_fast5_subset.TestFast5Subset.test_subset_from_multi) ... ok 267s test_subset_from_single (test.test_fast5_subset.TestFast5Subset.test_subset_from_single) ... ok 267s test_create_read (test.test_hardlink_metadata.TestHardlinkMetaData.test_create_read) ... ok 267s test_hardlink_multi_compression (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_multi_compression) ... ok 267s test_hardlink_single_to_multi (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_single_to_multi) ... ok 267s test_hardlink_subset (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset) ... ok 267s test_hardlink_subset_single_reads (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset_single_reads) ... ok 267s test_add_analysis (test.test_multi_fast5.TestMultiFast5.test_add_analysis) ... ok 267s test_channel_info (test.test_multi_fast5.TestMultiFast5.test_channel_info) ... ok 267s test_raw_data (test.test_multi_fast5.TestMultiFast5.test_raw_data) ... ok 267s test_read_interface (test.test_multi_fast5.TestMultiFast5.test_read_interface) ... ok 267s test_tracking_id (test.test_multi_fast5.TestMultiFast5.test_tracking_id) ... ok 267s test_001_raw_only (test.test_segmentation_tools.TestSegmentationTools.test_001_raw_only) ... ok 267s test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ok 267s 267s ---------------------------------------------------------------------- 267s Ran 76 tests in 1.751s 267s 267s OK (skipped=5) 267s autopkgtest [13:57:45]: test run-unit-test: -----------------------] 268s autopkgtest [13:57:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 268s run-unit-test PASS 268s autopkgtest [13:57:46]: @@@@@@@@@@@@@@@@@@@@ summary 268s run-unit-test PASS 285s nova [W] Using flock in prodstack6-arm64 285s flock: timeout while waiting to get lock 285s Creating nova instance adt-plucky-arm64-ont-fast5-api-20250315-135318-juju-7f2275-prod-proposed-migration-environment-20-fc2c2bdf-5462-4029-84ff-b0995811fc0d from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 285s nova [W] Timed out waiting for 1dc691d5-32bb-4755-9fd7-e136062c197b to get deleted.