0s autopkgtest [16:33:11]: starting date and time: 2024-11-18 16:33:11+0000 0s autopkgtest [16:33:11]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:33:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._83e_v0u/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:openmpi,src:sphinx-rtd-theme --apt-upgrade ont-fast5-api --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu1 openmpi/5.0.5-6 sphinx-rtd-theme/3.0.2+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-25.secgroup --name adt-plucky-arm64-ont-fast5-api-20241118-163311-juju-7f2275-prod-proposed-migration-environment-20-9d6b3750-7285-466f-abbc-78da64d814d6 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 97s autopkgtest [16:34:48]: testbed dpkg architecture: arm64 97s autopkgtest [16:34:48]: testbed apt version: 2.9.8 97s autopkgtest [16:34:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 98s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 98s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 99s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 99s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 99s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [103 kB] 99s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 99s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [638 kB] 99s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6696 B] 100s Fetched 1778 kB in 2s (1020 kB/s) 100s Reading package lists... 103s Reading package lists... 104s Building dependency tree... 104s Reading state information... 105s Calculating upgrade... 105s The following NEW packages will be installed: 105s liblsof0 105s The following packages will be upgraded: 105s libnvme1t64 linux-firmware lsof 106s 3 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 538 MB of archives. 106s After this operation, 1548 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.3+dfsg-2 [53.5 kB] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.3+dfsg-2 [235 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libnvme1t64 arm64 1.11.1-1 [83.7 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 linux-firmware arm64 20241118.git6e4e94b0-0ubuntu1 [537 MB] 222s Fetched 538 MB in 1min 56s (4638 kB/s) 222s Selecting previously unselected package liblsof0. 222s (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 ... 79972 files and directories currently installed.) 222s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_arm64.deb ... 222s Unpacking liblsof0 (4.99.3+dfsg-2) ... 222s Preparing to unpack .../lsof_4.99.3+dfsg-2_arm64.deb ... 222s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 223s Preparing to unpack .../libnvme1t64_1.11.1-1_arm64.deb ... 223s Unpacking libnvme1t64 (1.11.1-1) over (1.11-2) ... 223s Preparing to unpack .../linux-firmware_20241118.git6e4e94b0-0ubuntu1_arm64.deb ... 223s Unpacking linux-firmware (20241118.git6e4e94b0-0ubuntu1) over (20241108.git3bbb13a7-0ubuntu1) ... 227s Setting up linux-firmware (20241118.git6e4e94b0-0ubuntu1) ... 227s Setting up liblsof0 (4.99.3+dfsg-2) ... 227s Setting up libnvme1t64 (1.11.1-1) ... 227s Setting up lsof (4.99.3+dfsg-2) ... 227s Processing triggers for man-db (2.13.0-1) ... 228s Processing triggers for libc-bin (2.40-1ubuntu3) ... 228s Processing triggers for initramfs-tools (0.142ubuntu35) ... 228s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 228s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 255s System running in EFI mode, skipping. 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 257s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 257s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 257s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 257s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 257s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 259s Reading package lists... 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 260s Calculating upgrade... 261s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 261s Reading package lists... 261s Building dependency tree... 261s Reading state information... 262s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 263s autopkgtest [16:37:34]: rebooting testbed after setup commands that affected boot 267s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 289s autopkgtest [16:38:00]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 292s autopkgtest [16:38:03]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 294s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (dsc) [2236 B] 294s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (tar) [1384 kB] 294s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (diff) [4572 B] 295s gpgv: Signature made Wed Aug 28 16:17:26 2024 UTC 295s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 295s gpgv: issuer "tchet@debian.org" 295s gpgv: Can't check signature: No public key 295s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.1+dfsg-4.dsc: no acceptable signature found 295s autopkgtest [16:38:06]: testing package ont-fast5-api version 4.1.1+dfsg-4 295s autopkgtest [16:38:06]: build not needed 296s autopkgtest [16:38:07]: test run-unit-test: preparing testbed 297s Reading package lists... 297s Building dependency tree... 297s Reading state information... 297s Starting pkgProblemResolver with broken count: 0 298s Starting 2 pkgProblemResolver with broken count: 0 298s Done 298s The following additional packages will be installed: 298s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 298s liblzf1 libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api 298s python3-all python3-h5py python3-h5py-serial python3-numpy python3-packaging 298s python3-progressbar 298s Suggested packages: 298s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 298s The following NEW packages will be installed: 298s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 298s libhdf5-hl-100t64 liblapack3 liblzf1 libsz2 libvbz-hdf-plugin-dev 298s libvbz-hdf-plugin0t64 ont-fast5-api python3-all python3-h5py 298s python3-h5py-serial python3-numpy python3-packaging python3-progressbar 298s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 298s Need to get 9931 kB/9932 kB of archives. 298s After this operation, 51.0 MB of additional disk space will be used. 298s Get:1 /tmp/autopkgtest.r2zMzr/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 298s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 299s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 299s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 299s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 299s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 299s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 299s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 299s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 299s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin0t64 arm64 1.0.2-3.1build1 [18.2 kB] 299s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin-dev arm64 1.0.2-3.1build1 [14.4 kB] 299s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 299s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu1 [1449 kB] 299s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py all 3.11.0-8ubuntu1 [7982 B] 299s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 299s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-progressbar all 2.5-4 [11.0 kB] 299s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 ont-fast5-api arm64 4.1.1+dfsg-4 [47.7 kB] 299s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 300s Fetched 9931 kB in 1s (9912 kB/s) 300s Selecting previously unselected package libaec0:arm64. 300s (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 ... 80002 files and directories currently installed.) 300s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 300s Unpacking libaec0:arm64 (1.1.3-1) ... 300s Selecting previously unselected package libblas3:arm64. 300s Preparing to unpack .../01-libblas3_3.12.0-3build2_arm64.deb ... 300s Unpacking libblas3:arm64 (3.12.0-3build2) ... 300s Selecting previously unselected package libgfortran5:arm64. 300s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 300s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 300s Selecting previously unselected package libsz2:arm64. 300s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 300s Unpacking libsz2:arm64 (1.1.3-1) ... 300s Selecting previously unselected package libhdf5-103-1t64:arm64. 300s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 300s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 300s Selecting previously unselected package libhdf5-hl-100t64:arm64. 300s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 300s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 301s Selecting previously unselected package liblapack3:arm64. 301s Preparing to unpack .../06-liblapack3_3.12.0-3build2_arm64.deb ... 301s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 301s Selecting previously unselected package liblzf1:arm64. 301s Preparing to unpack .../07-liblzf1_3.6-4_arm64.deb ... 301s Unpacking liblzf1:arm64 (3.6-4) ... 301s Selecting previously unselected package libvbz-hdf-plugin0t64:arm64. 301s Preparing to unpack .../08-libvbz-hdf-plugin0t64_1.0.2-3.1build1_arm64.deb ... 301s Unpacking libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 301s Selecting previously unselected package libvbz-hdf-plugin-dev:arm64. 301s Preparing to unpack .../09-libvbz-hdf-plugin-dev_1.0.2-3.1build1_arm64.deb ... 301s Unpacking libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 301s Selecting previously unselected package python3-numpy. 301s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 301s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 301s Selecting previously unselected package python3-h5py-serial. 301s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu1_arm64.deb ... 301s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 301s Selecting previously unselected package python3-h5py. 301s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu1_all.deb ... 301s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 301s Selecting previously unselected package python3-packaging. 301s Preparing to unpack .../13-python3-packaging_24.2-1_all.deb ... 301s Unpacking python3-packaging (24.2-1) ... 301s Selecting previously unselected package python3-progressbar. 301s Preparing to unpack .../14-python3-progressbar_2.5-4_all.deb ... 301s Unpacking python3-progressbar (2.5-4) ... 301s Selecting previously unselected package ont-fast5-api. 301s Preparing to unpack .../15-ont-fast5-api_4.1.1+dfsg-4_arm64.deb ... 301s Unpacking ont-fast5-api (4.1.1+dfsg-4) ... 301s Selecting previously unselected package python3-all. 302s Preparing to unpack .../16-python3-all_3.12.6-0ubuntu1_arm64.deb ... 302s Unpacking python3-all (3.12.6-0ubuntu1) ... 302s Selecting previously unselected package autopkgtest-satdep. 302s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 302s Unpacking autopkgtest-satdep (0) ... 302s Setting up python3-all (3.12.6-0ubuntu1) ... 302s Setting up libaec0:arm64 (1.1.3-1) ... 302s Setting up libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 302s Setting up python3-progressbar (2.5-4) ... 302s Setting up libblas3:arm64 (3.12.0-3build2) ... 302s 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 302s Setting up python3-packaging (24.2-1) ... 302s Setting up liblzf1:arm64 (3.6-4) ... 302s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 302s Setting up libsz2:arm64 (1.1.3-1) ... 302s Setting up liblapack3:arm64 (3.12.0-3build2) ... 302s 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 302s Setting up libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 302s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 304s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 304s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 304s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 304s Setting up python3-h5py (3.11.0-8ubuntu1) ... 305s Setting up ont-fast5-api (4.1.1+dfsg-4) ... 305s Setting up autopkgtest-satdep (0) ... 305s Processing triggers for man-db (2.13.0-1) ... 305s Processing triggers for libc-bin (2.40-1ubuntu3) ... 309s (Reading database ... 81197 files and directories currently installed.) 309s Removing autopkgtest-satdep (0) ... 310s autopkgtest [16:38:21]: test run-unit-test: [----------------------- 311s test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ... ok 311s test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ... ok 311s test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ... ok 311s test_check_multi_read (test.test_check_compression.TestCheckCompression.test_check_multi_read) ... ok 311s test_check_read_compression_multi_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_multi_read) ... ok 311s test_check_read_compression_single_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_single_read) ... ok 311s test_check_read_compression_vbz (test.test_check_compression.TestCheckCompression.test_check_read_compression_vbz) ... ok 311s test_check_single_read_folder (test.test_check_compression.TestCheckCompression.test_check_single_read_folder) ... ok 311s test_multi_to_multi (test.test_compress_fast5.TestSanitise.test_multi_to_multi) ... ok 311s test_single_to_multi (test.test_compress_fast5.TestSanitise.test_single_to_multi) ... ok 311s test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert.test_add_read_from_multi) ... ok 311s test_compress_in_place (test.test_compress_fast5.TestVbzConvert.test_compress_in_place) ... skipped 'Permission Denied - to open folder' 311s test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert.test_compress_read_from_single) ... ok 311s test_conversion_script_multi (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi) ... skipped 'Permission Denied - to open folder' 311s test_conversion_script_multi_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi_retains_end_reason_enumeration) 311s Test that given a collection of multi read fast5 files that undergo compression ... ok 311s test_conversion_script_single (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single) ... skipped 'Permission Denied - to open folder' 311s test_conversion_script_single_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single_retains_end_reason_enumeration) 311s Test that given a collection of single read fast5 files that undergo compression ... ok 311s test_read_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_read_vbz_using_api) ... ok 311s test_write_vbz_directly (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_directly) ... skipped 'Tries to create dataset - permission denied' 311s test_write_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api) ... ok 311s test_write_vbz_using_api_single_read (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api_single_read) ... ok 311s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ok 311s test__clean (test.test_data_sanitisation.TestDataSanitisation.test__clean) ... ok 311s test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ... ok 311s test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ... ok 311s test_real_example_file (test.test_data_sanitisation.TestDataSanitisation.test_real_example_file) ... ok 311s test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ... ok 311s test_demux_1t (test.test_demux_fast5.TestDemuxFast5.test_demux_1t) ... ok 312s test_demux_8t (test.test_demux_fast5.TestDemuxFast5.test_demux_8t) ... ok 312s test_parse_summary (test.test_demux_fast5.TestDemuxFast5.test_parse_summary) ... ok 312s test_001_read_events (test.test_event_detection_tools.TestEventDetectionTools.test_001_read_events) ... ok 312s test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ... ok 312s test_yield_fast5_files_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_dir) ... ok 312s test_yield_fast5_files_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_fast5_file) ... ok 312s test_yield_fast5_reads_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_dir) ... ok 312s test_yield_fast5_reads_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_fast5_file) ... ok 312s test_yield_fast5_reads_set_versus_list_equality (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_set_versus_list_equality) ... ok 312s test_yield_fast5_reads_type_error (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_type_error) ... ok 312s test_yield_fast5_reads_with_empty_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_empty_set) ... ok 312s test_yield_fast5_reads_with_garbage_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_garbage_set) ... ok 312s test_yield_fast5_reads_with_list (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_list) ... ok 312s test_yield_fast5_reads_with_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_set) ... ok 312s test_add_read_to_multi (test.test_fast5_converter.TestFast5Converter.test_add_read_to_multi) ... ok 312s test_multi_to_single (test.test_fast5_converter.TestFast5Converter.test_multi_to_single) ... ok 312s test_multi_to_single_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_multi_to_single_incorrect_types) ... ok 312s test_single_to_multi (test.test_fast5_converter.TestFast5Converter.test_single_to_multi) ... skipped 'Permission Denied - to open folder' 312s test_single_to_multi_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_single_to_multi_incorrect_types) ... ok 312s test_001_get_latest_analysis (test.test_fast5_file.TestFast5File.test_001_get_latest_analysis) ... ok 312s test_002_add_analysis_group (test.test_fast5_file.TestFast5File.test_002_add_analysis_group) ... ok 312s test_002_read_summary_data (test.test_fast5_file.TestFast5File.test_002_read_summary_data) ... ok 312s test_003_add_analysis_subgroup (test.test_fast5_file.TestFast5File.test_003_add_analysis_subgroup) ... ok 312s test_010_v0_6_single (test.test_fast5_file.TestFast5File.test_010_v0_6_single) ... ok 312s test_011_v0_6_raw (test.test_fast5_file.TestFast5File.test_011_v0_6_raw) ... ok 312s test_012_v1_0_single (test.test_fast5_file.TestFast5File.test_012_v1_0_single) ... ok 312s test_fast5_add_analysis_dataset (test.test_fast5_file.TestFast5File.test_fast5_add_analysis_dataset) ... ok 312s test_fast5_add_and_get_chain (test.test_fast5_file.TestFast5File.test_fast5_add_and_get_chain) ... ok 312s test_fast5_add_group (test.test_fast5_file.TestFast5File.test_fast5_add_group) ... ok 312s test_fast5_set_analysis_config (test.test_fast5_file.TestFast5File.test_fast5_set_analysis_config) ... ok 312s test_correct_type (test.test_fast5_interface.TestFast5Interface.test_correct_type) ... ok 312s test_extract_selected_reads (test.test_fast5_subset.TestFast5Subset.test_extract_selected_reads) ... ok 312s test_read_generator (test.test_fast5_subset.TestFast5Subset.test_read_generator) ... ok 312s test_selector_args_generator (test.test_fast5_subset.TestFast5Subset.test_selector_args_generator) ... ok 312s test_subset_from_multi (test.test_fast5_subset.TestFast5Subset.test_subset_from_multi) ... ok 312s test_subset_from_single (test.test_fast5_subset.TestFast5Subset.test_subset_from_single) ... ok 312s test_create_read (test.test_hardlink_metadata.TestHardlinkMetaData.test_create_read) ... ok 312s test_hardlink_multi_compression (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_multi_compression) ... ok 312s test_hardlink_single_to_multi (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_single_to_multi) ... ok 313s test_hardlink_subset (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset) ... ok 313s test_hardlink_subset_single_reads (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset_single_reads) ... ok 313s test_add_analysis (test.test_multi_fast5.TestMultiFast5.test_add_analysis) ... ok 313s test_channel_info (test.test_multi_fast5.TestMultiFast5.test_channel_info) ... ok 313s test_raw_data (test.test_multi_fast5.TestMultiFast5.test_raw_data) ... ok 313s test_read_interface (test.test_multi_fast5.TestMultiFast5.test_read_interface) ... ok 313s test_tracking_id (test.test_multi_fast5.TestMultiFast5.test_tracking_id) ... ok 313s test_001_raw_only (test.test_segmentation_tools.TestSegmentationTools.test_001_raw_only) ... ok 313s test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ok 313s 313s ---------------------------------------------------------------------- 313s Ran 76 tests in 1.814s 313s 313s OK (skipped=5) 313s autopkgtest [16:38:24]: test run-unit-test: -----------------------] 314s run-unit-test PASS 314s autopkgtest [16:38:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 314s autopkgtest [16:38:25]: @@@@@@@@@@@@@@@@@@@@ summary 314s run-unit-test PASS 325s nova [W] Skipping flock in bos03-arm64 325s Creating nova instance adt-plucky-arm64-ont-fast5-api-20241118-163311-juju-7f2275-prod-proposed-migration-environment-20-9d6b3750-7285-466f-abbc-78da64d814d6 from image adt/ubuntu-plucky-arm64-server-20241117.img (UUID 346584db-208f-4446-ae16-5eaab5e37305)...