0s autopkgtest [09:45:46]: starting date and time: 2024-11-13 09:45:46+0000 0s autopkgtest [09:45:46]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:45:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.88zcy8b6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade ont-fast5-api --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-30.secgroup --name adt-plucky-arm64-ont-fast5-api-20241113-094546-juju-7f2275-prod-proposed-migration-environment-2-c33df6a5-8b48-41b8-8bed-20ace8b29109 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 82s autopkgtest [09:47:08]: testbed dpkg architecture: arm64 82s autopkgtest [09:47:08]: testbed apt version: 2.9.8 82s autopkgtest [09:47:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 84s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 84s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 84s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 84s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 84s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 84s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 84s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 84s Fetched 1794 kB in 1s (1901 kB/s) 84s Reading package lists... 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 89s The following NEW packages will be installed: 89s python3.13-gdbm 89s The following packages will be upgraded: 89s libpython3-stdlib python3 python3-gdbm python3-minimal 89s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 101 kB of archives. 89s After this operation, 141 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 90s Fetched 101 kB in 0s (282 kB/s) 90s (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 ... 79924 files and directories currently installed.) 90s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 90s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Setting up python3-minimal (3.12.7-1) ... 91s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 91s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 91s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 91s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 91s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 91s Selecting previously unselected package python3.13-gdbm. 91s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 91s Unpacking python3.13-gdbm (3.13.0-2) ... 91s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 91s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 91s Setting up python3.13-gdbm (3.13.0-2) ... 91s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 91s Setting up python3 (3.12.7-1) ... 91s Setting up python3-gdbm:arm64 (3.12.7-1) ... 91s Processing triggers for man-db (2.12.1-3) ... 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 94s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 95s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 96s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [09:47:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 102s autopkgtest [09:47:28]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (dsc) [2236 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (tar) [1384 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (diff) [4572 B] 104s gpgv: Signature made Wed Aug 28 16:17:26 2024 UTC 104s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 104s gpgv: issuer "tchet@debian.org" 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.1+dfsg-4.dsc: no acceptable signature found 105s autopkgtest [09:47:31]: testing package ont-fast5-api version 4.1.1+dfsg-4 105s autopkgtest [09:47:31]: build not needed 106s autopkgtest [09:47:32]: test run-unit-test: preparing testbed 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 109s The following additional packages will be installed: 109s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 109s liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2 109s libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api python3-all 109s python3-h5py python3-h5py-serial python3-numpy python3-packaging 109s python3-progressbar python3.13 python3.13-minimal 109s Suggested packages: 109s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 109s python3.13-venv python3.13-doc binfmt-support 109s The following NEW packages will be installed: 109s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 109s libhdf5-hl-100t64 liblapack3 liblzf1 libpython3.13-minimal 109s libpython3.13-stdlib libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 109s ont-fast5-api python3-all python3-h5py python3-h5py-serial python3-numpy 109s python3-packaging python3-progressbar python3.13 python3.13-minimal 109s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 14.8 MB/14.8 MB of archives. 109s After this operation, 62.6 MB of additional disk space will be used. 109s Get:1 /tmp/autopkgtest.GD0lpP/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 109s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 110s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 110s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 110s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 110s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 110s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 110s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin0t64 arm64 1.0.2-3.1build1 [18.2 kB] 110s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 libvbz-hdf-plugin-dev arm64 1.0.2-3.1build1 [14.4 kB] 110s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 110s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 110s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 110s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 110s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-progressbar all 2.5-4 [11.0 kB] 110s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 ont-fast5-api arm64 4.1.1+dfsg-4 [47.7 kB] 110s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 110s Get:22 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 111s Fetched 14.8 MB in 1s (11.6 MB/s) 111s Selecting previously unselected package libpython3.13-minimal:arm64. 111s (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 ... 79931 files and directories currently installed.) 111s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 111s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 111s Selecting previously unselected package python3.13-minimal. 111s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 111s Unpacking python3.13-minimal (3.13.0-2) ... 111s Selecting previously unselected package libaec0:arm64. 111s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 111s Unpacking libaec0:arm64 (1.1.3-1) ... 111s Selecting previously unselected package libblas3:arm64. 111s Preparing to unpack .../03-libblas3_3.12.0-3build2_arm64.deb ... 111s Unpacking libblas3:arm64 (3.12.0-3build2) ... 111s Selecting previously unselected package libgfortran5:arm64. 111s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 111s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 111s Selecting previously unselected package libsz2:arm64. 111s Preparing to unpack .../05-libsz2_1.1.3-1_arm64.deb ... 111s Unpacking libsz2:arm64 (1.1.3-1) ... 111s Selecting previously unselected package libhdf5-103-1t64:arm64. 111s Preparing to unpack .../06-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 111s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 111s Selecting previously unselected package libhdf5-hl-100t64:arm64. 111s Preparing to unpack .../07-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 111s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 111s Selecting previously unselected package liblapack3:arm64. 111s Preparing to unpack .../08-liblapack3_3.12.0-3build2_arm64.deb ... 111s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 111s Selecting previously unselected package liblzf1:arm64. 111s Preparing to unpack .../09-liblzf1_3.6-4_arm64.deb ... 111s Unpacking liblzf1:arm64 (3.6-4) ... 111s Selecting previously unselected package libpython3.13-stdlib:arm64. 111s Preparing to unpack .../10-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 111s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 111s Selecting previously unselected package libvbz-hdf-plugin0t64:arm64. 111s Preparing to unpack .../11-libvbz-hdf-plugin0t64_1.0.2-3.1build1_arm64.deb ... 111s Unpacking libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 111s Selecting previously unselected package libvbz-hdf-plugin-dev:arm64. 111s Preparing to unpack .../12-libvbz-hdf-plugin-dev_1.0.2-3.1build1_arm64.deb ... 111s Unpacking libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 111s Selecting previously unselected package python3-numpy. 112s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 112s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 112s Selecting previously unselected package python3-h5py-serial. 112s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 112s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 112s Selecting previously unselected package python3-h5py. 112s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ... 112s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 112s Selecting previously unselected package python3-packaging. 112s Preparing to unpack .../16-python3-packaging_24.1-1_all.deb ... 112s Unpacking python3-packaging (24.1-1) ... 112s Selecting previously unselected package python3-progressbar. 112s Preparing to unpack .../17-python3-progressbar_2.5-4_all.deb ... 112s Unpacking python3-progressbar (2.5-4) ... 112s Selecting previously unselected package ont-fast5-api. 112s Preparing to unpack .../18-ont-fast5-api_4.1.1+dfsg-4_arm64.deb ... 112s Unpacking ont-fast5-api (4.1.1+dfsg-4) ... 112s Selecting previously unselected package python3.13. 112s Preparing to unpack .../19-python3.13_3.13.0-2_arm64.deb ... 112s Unpacking python3.13 (3.13.0-2) ... 112s Selecting previously unselected package python3-all. 112s Preparing to unpack .../20-python3-all_3.12.7-1_arm64.deb ... 112s Unpacking python3-all (3.12.7-1) ... 112s Selecting previously unselected package autopkgtest-satdep. 112s Preparing to unpack .../21-1-autopkgtest-satdep.deb ... 112s Unpacking autopkgtest-satdep (0) ... 112s Setting up libaec0:arm64 (1.1.3-1) ... 112s Setting up libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1build1) ... 112s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 112s Setting up python3-progressbar (2.5-4) ... 112s Setting up libblas3:arm64 (3.12.0-3build2) ... 112s 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 112s Setting up python3-packaging (24.1-1) ... 113s Setting up liblzf1:arm64 (3.6-4) ... 113s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 113s Setting up python3.13-minimal (3.13.0-2) ... 114s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 114s Setting up libsz2:arm64 (1.1.3-1) ... 114s Setting up liblapack3:arm64 (3.12.0-3build2) ... 114s 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 114s Setting up libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1build1) ... 114s Setting up python3.13 (3.13.0-2) ... 115s Setting up python3-all (3.12.7-1) ... 115s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 119s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 119s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 119s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 120s Setting up python3-h5py (3.11.0-5ubuntu1) ... 120s Setting up ont-fast5-api (4.1.1+dfsg-4) ... 120s Setting up autopkgtest-satdep (0) ... 120s Processing triggers for systemd (256.5-2ubuntu4) ... 121s Processing triggers for man-db (2.12.1-3) ... 121s Processing triggers for libc-bin (2.40-1ubuntu3) ... 125s (Reading database ... 81813 files and directories currently installed.) 125s Removing autopkgtest-satdep (0) ... 126s autopkgtest [09:47:52]: test run-unit-test: [----------------------- 126s test.test_alignment_tools (unittest.loader._FailedTest.test.test_alignment_tools) ... ERROR 126s test.test_basecall_1d_tools (unittest.loader._FailedTest.test.test_basecall_1d_tools) ... ERROR 126s test.test_basecall_2d_tools (unittest.loader._FailedTest.test.test_basecall_2d_tools) ... ERROR 126s test.test_check_compression (unittest.loader._FailedTest.test.test_check_compression) ... ERROR 126s test.test_compress_fast5 (unittest.loader._FailedTest.test.test_compress_fast5) ... ERROR 126s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ERROR 126s test.test_data_sanitisation (unittest.loader._FailedTest.test.test_data_sanitisation) ... ERROR 126s test.test_demux_fast5 (unittest.loader._FailedTest.test.test_demux_fast5) ... ERROR 127s test.test_event_detection_tools (unittest.loader._FailedTest.test.test_event_detection_tools) ... ERROR 127s test.test_fast5_conversion_utils (unittest.loader._FailedTest.test.test_fast5_conversion_utils) ... ERROR 127s test.test_fast5_converter (unittest.loader._FailedTest.test.test_fast5_converter) ... ERROR 127s test.test_fast5_file (unittest.loader._FailedTest.test.test_fast5_file) ... ERROR 127s test.test_fast5_interface (unittest.loader._FailedTest.test.test_fast5_interface) ... ERROR 127s test.test_fast5_subset (unittest.loader._FailedTest.test.test_fast5_subset) ... ERROR 127s test.test_hardlink_metadata (unittest.loader._FailedTest.test.test_hardlink_metadata) ... ERROR 127s test.test_multi_fast5 (unittest.loader._FailedTest.test.test_multi_fast5) ... ERROR 127s test.test_segmentation_tools (unittest.loader._FailedTest.test.test_segmentation_tools) ... ERROR 127s 127s ====================================================================== 127s ERROR: test.test_alignment_tools (unittest.loader._FailedTest.test.test_alignment_tools) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_alignment_tools 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_alignment_tools.py", line 2, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_basecall_1d_tools (unittest.loader._FailedTest.test.test_basecall_1d_tools) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_basecall_1d_tools 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_basecall_1d_tools.py", line 1, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_basecall_2d_tools (unittest.loader._FailedTest.test.test_basecall_2d_tools) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_basecall_2d_tools 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_basecall_2d_tools.py", line 1, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_check_compression (unittest.loader._FailedTest.test.test_check_compression) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_check_compression 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_check_compression.py", line 4, in 127s import numpy 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_compress_fast5 (unittest.loader._FailedTest.test.test_compress_fast5) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_compress_fast5 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_compress_fast5.py", line 1, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) 127s ---------------------------------------------------------------------- 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_compression_settings.py", line 11, in test_register_plugin_no_prepend 127s with patch('h5py.h5pl', create=True) as mock: 127s ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^ 127s File "/usr/lib/python3.13/unittest/mock.py", line 1475, in __enter__ 127s self.target = self.getter() 127s ~~~~~~~~~~~^^ 127s File "/usr/lib/python3.13/pkgutil.py", line 513, in resolve_name 127s mod = importlib.import_module(modname) 127s File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module 127s return _bootstrap._gcd_import(name[level:], package, level) 127s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 127s File "", line 1387, in _gcd_import 127s File "", line 1360, in _find_and_load 127s File "", line 1331, in _find_and_load_unlocked 127s File "", line 935, in _load_unlocked 127s File "", line 1022, in exec_module 127s File "", line 488, in _call_with_frames_removed 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s ====================================================================== 127s ERROR: test.test_data_sanitisation (unittest.loader._FailedTest.test.test_data_sanitisation) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_data_sanitisation 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_data_sanitisation.py", line 1, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_demux_fast5 (unittest.loader._FailedTest.test.test_demux_fast5) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_demux_fast5 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_demux_fast5.py", line 4, in 127s from ont_fast5_api.conversion_tools.demux_fast5 import Fast5Demux 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/demux_fast5.py", line 16, in 127s from ont_fast5_api.conversion_tools.conversion_utils import ( 127s ...<6 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/conversion_utils.py", line 12, in 127s from ont_fast5_api.fast5_interface import get_fast5_file 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_interface.py", line 2, in 127s from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_event_detection_tools (unittest.loader._FailedTest.test.test_event_detection_tools) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_event_detection_tools 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_event_detection_tools.py", line 2, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_fast5_conversion_utils (unittest.loader._FailedTest.test.test_fast5_conversion_utils) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_fast5_conversion_utils 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_fast5_conversion_utils.py", line 2, in 127s from ont_fast5_api.fast5_read import Fast5Read 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_read.py", line 4, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_fast5_converter (unittest.loader._FailedTest.test.test_fast5_converter) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_fast5_converter 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_fast5_converter.py", line 5, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_fast5_file (unittest.loader._FailedTest.test.test_fast5_file) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_fast5_file 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_fast5_file.py", line 11, in 127s from ont_fast5_api.fast5_info import Fast5Info, _clean 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_info.py", line 4, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_fast5_interface (unittest.loader._FailedTest.test.test_fast5_interface) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_fast5_interface 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_fast5_interface.py", line 4, in 127s from ont_fast5_api.fast5_file import Fast5File 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_fast5_subset (unittest.loader._FailedTest.test.test_fast5_subset) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_fast5_subset 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_fast5_subset.py", line 2, in 127s import numpy 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_hardlink_metadata (unittest.loader._FailedTest.test.test_hardlink_metadata) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_hardlink_metadata 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 127s from . import _debian_h5py_serial as _h5py 127s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 127s from . import _errors 127s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_hardlink_metadata.py", line 4, in 127s from ont_fast5_api.conversion_tools.compress_fast5 import compress_file 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/compress_fast5.py", line 9, in 127s from ont_fast5_api.conversion_tools.conversion_utils import get_fast5_file_list, get_progress_bar 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/conversion_utils.py", line 12, in 127s from ont_fast5_api.fast5_interface import get_fast5_file 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_interface.py", line 2, in 127s from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError 127s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 127s import h5py 127s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 127s from . import _debian_h5py_mpi as _h5py 127s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 127s 127s 127s ====================================================================== 127s ERROR: test.test_multi_fast5 (unittest.loader._FailedTest.test.test_multi_fast5) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_multi_fast5 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_multi_fast5.py", line 1, in 127s import numpy 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ====================================================================== 127s ERROR: test.test_segmentation_tools (unittest.loader._FailedTest.test.test_segmentation_tools) 127s ---------------------------------------------------------------------- 127s ImportError: Failed to import test module: test.test_segmentation_tools 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 127s from . import multiarray 127s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 127s from . import overrides 127s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 127s from numpy.core._multiarray_umath import ( 127s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 127s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 127s 127s During handling of the above exception, another exception occurred: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 127s from numpy.__config__ import show as show_config 127s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 127s from numpy.core._multiarray_umath import ( 127s ...<3 lines>... 127s ) 127s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 127s raise ImportError(msg) 127s ImportError: 127s 127s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 127s 127s Importing the numpy C-extensions failed. This error can happen for 127s many reasons, often due to issues with your setup or how NumPy was 127s installed. 127s 127s We have compiled some common reasons and troubleshooting tips at: 127s 127s https://numpy.org/devdocs/user/troubleshooting-importerror.html 127s 127s Please note and check the following: 127s 127s * The Python version is: Python3.13 from "/usr/bin/python3.13" 127s * The NumPy version is: "1.26.4" 127s 127s and make sure that they are the versions you expect. 127s Please carefully study the documentation linked above for further help. 127s 127s Original error was: No module named 'numpy.core._multiarray_umath' 127s 127s 127s The above exception was the direct cause of the following exception: 127s 127s Traceback (most recent call last): 127s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 127s module = self._get_module_from_name(name) 127s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 127s __import__(name) 127s ~~~~~~~~~~^^^^^^ 127s File "/tmp/autopkgtest.GD0lpP/autopkgtest_tmp/test/test_segmentation_tools.py", line 2, in 127s import numpy as np 127s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 127s raise ImportError(msg) from e 127s ImportError: Error importing numpy: you should not try to import numpy from 127s its source directory; please exit the numpy source tree, and relaunch 127s your python interpreter from there. 127s 127s 127s ---------------------------------------------------------------------- 127s Ran 17 tests in 0.006s 127s 127s FAILED (errors=17) 127s autopkgtest [09:47:53]: test run-unit-test: -----------------------] 127s autopkgtest [09:47:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 127s run-unit-test FAIL non-zero exit status 1 128s autopkgtest [09:47:54]: @@@@@@@@@@@@@@@@@@@@ summary 128s run-unit-test FAIL non-zero exit status 1 142s virt: nova [W] Skipping flock in bos03-arm64 142s virt: Creating nova instance adt-plucky-arm64-ont-fast5-api-20241113-094546-juju-7f2275-prod-proposed-migration-environment-2-c33df6a5-8b48-41b8-8bed-20ace8b29109 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...