0s autopkgtest [21:42:27]: starting date and time: 2024-03-13 21:42:27+0000 0s autopkgtest [21:42:27]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:42:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ims35enn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:hdf5,src:openmpi,src:openssl,src:pmix --apt-upgrade ont-fast5-api --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.10.0-1ubuntu2 hdf5/1.10.10+repack-3.1ubuntu2 openmpi/4.1.6-5.1ubuntu3 openssl/3.0.13-0ubuntu1 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-24.secgroup --name adt-noble-arm64-ont-fast5-api-20240313-214227-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 169s autopkgtest [21:45:16]: testbed dpkg architecture: arm64 169s autopkgtest [21:45:16]: testbed apt version: 2.7.12 169s autopkgtest [21:45:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 170s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 170s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 170s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 170s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 171s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 171s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 172s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 172s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 172s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 172s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 172s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 172s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 172s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 173s Fetched 7327 kB in 3s (2620 kB/s) 174s Reading package lists... 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Calculating upgrade... 178s The following packages will be REMOVED: 178s libssl3 178s The following NEW packages will be installed: 178s libssl3t64 178s The following packages will be upgraded: 178s console-setup console-setup-linux keyboard-configuration openssl 178s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 178s Need to get 4955 kB of archives. 178s After this operation, 74.8 kB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 179s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 179s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 179s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 179s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 180s Preconfiguring packages ... 180s Fetched 4955 kB in 1s (3704 kB/s) 181s (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 ... 74759 files and directories currently installed.) 181s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 181s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 181s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 181s wget depends on libssl3 (>= 3.0.0). 181s u-boot-tools depends on libssl3 (>= 3.0.0). 181s tnftp depends on libssl3 (>= 3.0.0). 181s tcpdump depends on libssl3 (>= 3.0.0). 181s systemd-resolved depends on libssl3 (>= 3.0.0). 181s systemd depends on libssl3 (>= 3.0.0). 181s sudo depends on libssl3 (>= 3.0.0). 181s sbsigntool depends on libssl3 (>= 3.0.0). 181s rsync depends on libssl3 (>= 3.0.0). 181s python3-cryptography depends on libssl3 (>= 3.0.0). 181s openssh-server depends on libssl3 (>= 3.0.10). 181s openssh-client depends on libssl3 (>= 3.0.10). 181s mtd-utils depends on libssl3 (>= 3.0.0). 181s mokutil depends on libssl3 (>= 3.0.0). 181s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 181s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 181s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 181s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 181s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 181s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 181s libnvme1 depends on libssl3 (>= 3.0.0). 181s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 181s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 181s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 181s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 181s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 181s kmod depends on libssl3 (>= 3.0.0). 181s dhcpcd-base depends on libssl3 (>= 3.0.0). 181s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 181s 181s (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 ... 74759 files and directories currently installed.) 181s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 181s Selecting previously unselected package libssl3t64:arm64. 181s (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 ... 74748 files and directories currently installed.) 181s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 181s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 181s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 181s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 181s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 181s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 181s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 181s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 181s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 181s Setting up keyboard-configuration (1.226ubuntu1) ... 182s Your console font configuration will be updated the next time your system 182s boots. If you want to update it now, run 'setupcon' from a virtual console. 182s update-initramfs: deferring update (trigger activated) 182s Setting up openssl (3.0.13-0ubuntu1) ... 182s Setting up console-setup-linux (1.226ubuntu1) ... 184s Setting up console-setup (1.226ubuntu1) ... 185s update-initramfs: deferring update (trigger activated) 185s Processing triggers for man-db (2.12.0-3) ... 185s Processing triggers for libc-bin (2.39-0ubuntu2) ... 186s Processing triggers for initramfs-tools (0.142ubuntu20) ... 186s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 186s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 205s System running in EFI mode, skipping. 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 207s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 207s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 207s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 208s Reading package lists... 208s Reading package lists... 209s Building dependency tree... 209s Reading state information... 209s Calculating upgrade... 210s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 212s autopkgtest [21:45:59]: rebooting testbed after setup commands that affected boot 473s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 482s autopkgtest [21:50:29]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 486s autopkgtest [21:50:33]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 489s Get:1 http://ftpmaster.internal/ubuntu noble/universe ont-fast5-api 4.1.1+dfsg-3build1 (dsc) [2273 B] 489s Get:2 http://ftpmaster.internal/ubuntu noble/universe ont-fast5-api 4.1.1+dfsg-3build1 (tar) [1384 kB] 489s Get:3 http://ftpmaster.internal/ubuntu noble/universe ont-fast5-api 4.1.1+dfsg-3build1 (diff) [4612 B] 489s gpgv: Signature made Thu Nov 2 19:23:51 2023 UTC 489s gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 489s gpgv: issuer "doko@ubuntu.com" 489s gpgv: Can't check signature: No public key 489s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.1+dfsg-3build1.dsc: no acceptable signature found 490s autopkgtest [21:50:37]: testing package ont-fast5-api version 4.1.1+dfsg-3build1 490s autopkgtest [21:50:37]: build not needed 490s autopkgtest [21:50:37]: test run-unit-test: preparing testbed 493s Reading package lists... 493s Building dependency tree... 493s Reading state information... 493s Starting pkgProblemResolver with broken count: 0 493s Starting 2 pkgProblemResolver with broken count: 0 493s Done 494s The following additional packages will be installed: 494s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 494s liblzf1 libpython3.11-minimal libpython3.11-stdlib libsz2 494s libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api python3-all 494s python3-distutils python3-h5py python3-h5py-serial python3-lib2to3 494s python3-numpy python3-packaging python3-progressbar python3.11 494s python3.11-minimal 494s Suggested packages: 494s python-h5py-doc gcc gfortran python3-dev python3-pytest python3.11-venv 494s python3.11-doc binfmt-support 494s The following NEW packages will be installed: 494s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 494s libhdf5-hl-100t64 liblapack3 liblzf1 libpython3.11-minimal 494s libpython3.11-stdlib libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 494s ont-fast5-api python3-all python3-distutils python3-h5py python3-h5py-serial 494s python3-lib2to3 python3-numpy python3-packaging python3-progressbar 494s python3.11 python3.11-minimal 494s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 494s Need to get 15.4 MB/15.4 MB of archives. 494s After this operation, 69.6 MB of additional disk space will be used. 494s Get:1 /tmp/autopkgtest.dpOB96/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 494s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 495s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 495s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 496s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 496s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 496s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 496s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 496s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 496s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 496s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 496s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 497s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 497s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libvbz-hdf-plugin0t64 arm64 1.0.2-3.1 [18.1 kB] 497s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libvbz-hdf-plugin-dev arm64 1.0.2-3.1 [14.4 kB] 497s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 497s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 497s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 497s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 497s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-progressbar all 2.5-4 [11.0 kB] 497s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 ont-fast5-api arm64 4.1.1+dfsg-3build1 [47.7 kB] 497s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] 497s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] 497s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 498s Fetched 15.4 MB in 3s (5486 kB/s) 498s Selecting previously unselected package libpython3.11-minimal:arm64. 498s (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 ... 74761 files and directories currently installed.) 498s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 498s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 498s Selecting previously unselected package python3.11-minimal. 498s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 498s Unpacking python3.11-minimal (3.11.8-1) ... 498s Selecting previously unselected package libpython3.11-stdlib:arm64. 498s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 498s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 499s Selecting previously unselected package python3.11. 499s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ... 499s Unpacking python3.11 (3.11.8-1) ... 499s Selecting previously unselected package libaec0:arm64. 499s Preparing to unpack .../04-libaec0_1.1.2-1_arm64.deb ... 499s Unpacking libaec0:arm64 (1.1.2-1) ... 499s Selecting previously unselected package libblas3:arm64. 499s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 499s Unpacking libblas3:arm64 (3.12.0-3) ... 499s Selecting previously unselected package libgfortran5:arm64. 499s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 499s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 499s Selecting previously unselected package libsz2:arm64. 499s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ... 499s Unpacking libsz2:arm64 (1.1.2-1) ... 499s Selecting previously unselected package libhdf5-103-1t64:arm64. 499s Preparing to unpack .../08-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 499s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 499s Selecting previously unselected package libhdf5-hl-100t64:arm64. 499s Preparing to unpack .../09-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 499s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 499s Selecting previously unselected package liblapack3:arm64. 499s Preparing to unpack .../10-liblapack3_3.12.0-3_arm64.deb ... 499s Unpacking liblapack3:arm64 (3.12.0-3) ... 499s Selecting previously unselected package liblzf1:arm64. 499s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 499s Unpacking liblzf1:arm64 (3.6-4) ... 499s Selecting previously unselected package libvbz-hdf-plugin0t64:arm64. 499s Preparing to unpack .../12-libvbz-hdf-plugin0t64_1.0.2-3.1_arm64.deb ... 500s Unpacking libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1) ... 500s Selecting previously unselected package libvbz-hdf-plugin-dev:arm64. 500s Preparing to unpack .../13-libvbz-hdf-plugin-dev_1.0.2-3.1_arm64.deb ... 500s Unpacking libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1) ... 500s Selecting previously unselected package python3-numpy. 500s Preparing to unpack .../14-python3-numpy_1%3a1.24.2-2_arm64.deb ... 500s Unpacking python3-numpy (1:1.24.2-2) ... 500s Selecting previously unselected package python3-h5py-serial. 500s Preparing to unpack .../15-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 500s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 500s Selecting previously unselected package python3-h5py. 500s Preparing to unpack .../16-python3-h5py_3.10.0-1ubuntu2_all.deb ... 500s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 500s Selecting previously unselected package python3-packaging. 500s Preparing to unpack .../17-python3-packaging_23.2-1_all.deb ... 500s Unpacking python3-packaging (23.2-1) ... 500s Selecting previously unselected package python3-progressbar. 500s Preparing to unpack .../18-python3-progressbar_2.5-4_all.deb ... 500s Unpacking python3-progressbar (2.5-4) ... 500s Selecting previously unselected package ont-fast5-api. 500s Preparing to unpack .../19-ont-fast5-api_4.1.1+dfsg-3build1_arm64.deb ... 500s Unpacking ont-fast5-api (4.1.1+dfsg-3build1) ... 500s Selecting previously unselected package python3-lib2to3. 500s Preparing to unpack .../20-python3-lib2to3_3.11.5-1_all.deb ... 500s Unpacking python3-lib2to3 (3.11.5-1) ... 500s Selecting previously unselected package python3-distutils. 500s Preparing to unpack .../21-python3-distutils_3.11.5-1_all.deb ... 500s Unpacking python3-distutils (3.11.5-1) ... 500s Selecting previously unselected package python3-all. 500s Preparing to unpack .../22-python3-all_3.12.1-0ubuntu2_arm64.deb ... 500s Unpacking python3-all (3.12.1-0ubuntu2) ... 500s Selecting previously unselected package autopkgtest-satdep. 500s Preparing to unpack .../23-1-autopkgtest-satdep.deb ... 500s Unpacking autopkgtest-satdep (0) ... 501s Setting up libaec0:arm64 (1.1.2-1) ... 501s Setting up libvbz-hdf-plugin0t64:arm64 (1.0.2-3.1) ... 501s Setting up python3-progressbar (2.5-4) ... 501s Setting up libblas3:arm64 (3.12.0-3) ... 501s 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 501s Setting up python3-packaging (23.2-1) ... 501s Setting up liblzf1:arm64 (3.6-4) ... 501s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 501s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 501s Setting up python3-lib2to3 (3.11.5-1) ... 502s Setting up libsz2:arm64 (1.1.2-1) ... 502s Setting up python3-distutils (3.11.5-1) ... 502s python3.12: can't get files for byte-compilation 502s Setting up python3.11-minimal (3.11.8-1) ... 502s Setting up liblapack3:arm64 (3.12.0-3) ... 502s 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 502s Setting up libvbz-hdf-plugin-dev:arm64 (1.0.2-3.1) ... 502s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 502s Setting up python3-all (3.12.1-0ubuntu2) ... 502s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 502s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 502s Setting up python3.11 (3.11.8-1) ... 503s Setting up python3-numpy (1:1.24.2-2) ... 505s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 505s Setting up python3-h5py (3.10.0-1ubuntu2) ... 506s Setting up ont-fast5-api (4.1.1+dfsg-3build1) ... 506s Setting up autopkgtest-satdep (0) ... 506s Processing triggers for systemd (255.2-3ubuntu2) ... 507s Processing triggers for man-db (2.12.0-3) ... 507s Processing triggers for libc-bin (2.39-0ubuntu2) ... 512s (Reading database ... 76943 files and directories currently installed.) 512s Removing autopkgtest-satdep (0) ... 513s autopkgtest [21:51:00]: test run-unit-test: [----------------------- 514s test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ... ok 514s test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ... ok 514s test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ... ok 514s test_check_multi_read (test.test_check_compression.TestCheckCompression.test_check_multi_read) ... ok 514s test_check_read_compression_multi_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_multi_read) ... ok 514s test_check_read_compression_single_read (test.test_check_compression.TestCheckCompression.test_check_read_compression_single_read) ... ok 514s test_check_read_compression_vbz (test.test_check_compression.TestCheckCompression.test_check_read_compression_vbz) ... ok 514s test_check_single_read_folder (test.test_check_compression.TestCheckCompression.test_check_single_read_folder) ... ok 514s test_multi_to_multi (test.test_compress_fast5.TestSanitise.test_multi_to_multi) ... ok 514s test_single_to_multi (test.test_compress_fast5.TestSanitise.test_single_to_multi) ... ok 514s test_add_read_from_multi (test.test_compress_fast5.TestVbzConvert.test_add_read_from_multi) ... ok 514s test_compress_in_place (test.test_compress_fast5.TestVbzConvert.test_compress_in_place) ... skipped 'Permission Denied - to open folder' 514s test_compress_read_from_single (test.test_compress_fast5.TestVbzConvert.test_compress_read_from_single) ... ok 514s test_conversion_script_multi (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi) ... skipped 'Permission Denied - to open folder' 514s test_conversion_script_multi_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_multi_retains_end_reason_enumeration) 514s Test that given a collection of multi read fast5 files that undergo compression ... ok 514s test_conversion_script_single (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single) ... skipped 'Permission Denied - to open folder' 514s test_conversion_script_single_retains_end_reason_enumeration (test.test_compress_fast5.TestVbzConvert.test_conversion_script_single_retains_end_reason_enumeration) 515s Test that given a collection of single read fast5 files that undergo compression ... ok 515s test_read_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_read_vbz_using_api) ... ok 515s test_write_vbz_directly (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_directly) ... skipped 'Tries to create dataset - permission denied' 515s test_write_vbz_using_api (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api) ... ok 515s test_write_vbz_using_api_single_read (test.test_compress_fast5.TestVbzReadWrite.test_write_vbz_using_api_single_read) ... ok 515s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ok 515s test__clean (test.test_data_sanitisation.TestDataSanitisation.test__clean) ... ok 515s test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ... ok 515s test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ... ok 515s test_real_example_file (test.test_data_sanitisation.TestDataSanitisation.test_real_example_file) ... ok 515s test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ... ok 515s test_demux_1t (test.test_demux_fast5.TestDemuxFast5.test_demux_1t) ... ok 516s test_demux_8t (test.test_demux_fast5.TestDemuxFast5.test_demux_8t) ... ok 516s test_parse_summary (test.test_demux_fast5.TestDemuxFast5.test_parse_summary) ... ok 516s test_001_read_events (test.test_event_detection_tools.TestEventDetectionTools.test_001_read_events) ... ok 516s test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ... ok 516s test_yield_fast5_files_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_dir) ... ok 516s test_yield_fast5_files_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_files_from_fast5_file) ... ok 516s test_yield_fast5_reads_from_dir (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_dir) ... ok 516s test_yield_fast5_reads_from_fast5_file (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_from_fast5_file) ... ok 516s test_yield_fast5_reads_set_versus_list_equality (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_set_versus_list_equality) ... ok 516s test_yield_fast5_reads_type_error (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_type_error) ... ok 516s test_yield_fast5_reads_with_empty_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_empty_set) ... ok 516s test_yield_fast5_reads_with_garbage_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_garbage_set) ... ok 516s test_yield_fast5_reads_with_list (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_list) ... ok 516s test_yield_fast5_reads_with_set (test.test_fast5_conversion_utils.TestFast5ConversionUtilities.test_yield_fast5_reads_with_set) ... ok 516s test_add_read_to_multi (test.test_fast5_converter.TestFast5Converter.test_add_read_to_multi) ... ok 516s test_multi_to_single (test.test_fast5_converter.TestFast5Converter.test_multi_to_single) ... ok 516s test_multi_to_single_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_multi_to_single_incorrect_types) ... ok 516s test_single_to_multi (test.test_fast5_converter.TestFast5Converter.test_single_to_multi) ... skipped 'Permission Denied - to open folder' 516s test_single_to_multi_incorrect_types (test.test_fast5_converter.TestFast5Converter.test_single_to_multi_incorrect_types) ... ok 516s test_001_get_latest_analysis (test.test_fast5_file.TestFast5File.test_001_get_latest_analysis) ... ok 516s test_002_add_analysis_group (test.test_fast5_file.TestFast5File.test_002_add_analysis_group) ... ok 516s test_002_read_summary_data (test.test_fast5_file.TestFast5File.test_002_read_summary_data) ... ok 516s test_003_add_analysis_subgroup (test.test_fast5_file.TestFast5File.test_003_add_analysis_subgroup) ... ok 516s test_010_v0_6_single (test.test_fast5_file.TestFast5File.test_010_v0_6_single) ... ok 516s test_011_v0_6_raw (test.test_fast5_file.TestFast5File.test_011_v0_6_raw) ... ok 516s test_012_v1_0_single (test.test_fast5_file.TestFast5File.test_012_v1_0_single) ... ok 516s test_fast5_add_analysis_dataset (test.test_fast5_file.TestFast5File.test_fast5_add_analysis_dataset) ... ok 516s test_fast5_add_and_get_chain (test.test_fast5_file.TestFast5File.test_fast5_add_and_get_chain) ... ok 516s test_fast5_add_group (test.test_fast5_file.TestFast5File.test_fast5_add_group) ... ok 516s test_fast5_set_analysis_config (test.test_fast5_file.TestFast5File.test_fast5_set_analysis_config) ... ok 516s test_correct_type (test.test_fast5_interface.TestFast5Interface.test_correct_type) ... ok 516s test_extract_selected_reads (test.test_fast5_subset.TestFast5Subset.test_extract_selected_reads) ... ok 516s test_read_generator (test.test_fast5_subset.TestFast5Subset.test_read_generator) ... ok 516s test_selector_args_generator (test.test_fast5_subset.TestFast5Subset.test_selector_args_generator) ... ok 516s test_subset_from_multi (test.test_fast5_subset.TestFast5Subset.test_subset_from_multi) ... ok 516s test_subset_from_single (test.test_fast5_subset.TestFast5Subset.test_subset_from_single) ... ok 516s test_create_read (test.test_hardlink_metadata.TestHardlinkMetaData.test_create_read) ... ok 516s test_hardlink_multi_compression (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_multi_compression) ... ok 516s test_hardlink_single_to_multi (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_single_to_multi) ... ok 516s test_hardlink_subset (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset) ... ok 516s test_hardlink_subset_single_reads (test.test_hardlink_metadata.TestHardlinkMetaData.test_hardlink_subset_single_reads) ... ok 516s test_add_analysis (test.test_multi_fast5.TestMultiFast5.test_add_analysis) ... ok 516s test_channel_info (test.test_multi_fast5.TestMultiFast5.test_channel_info) ... ok 516s test_raw_data (test.test_multi_fast5.TestMultiFast5.test_raw_data) ... ok 516s test_read_interface (test.test_multi_fast5.TestMultiFast5.test_read_interface) ... ok 516s test_tracking_id (test.test_multi_fast5.TestMultiFast5.test_tracking_id) ... ok 516s test_001_raw_only (test.test_segmentation_tools.TestSegmentationTools.test_001_raw_only) ... ok 516s test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ok 516s 516s ---------------------------------------------------------------------- 516s Ran 76 tests in 1.921s 516s 516s OK (skipped=5) 517s autopkgtest [21:51:04]: test run-unit-test: -----------------------] 517s autopkgtest [21:51:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 517s run-unit-test PASS 518s autopkgtest [21:51:05]: @@@@@@@@@@@@@@@@@@@@ summary 518s run-unit-test PASS 536s Creating nova instance adt-noble-arm64-ont-fast5-api-20240313-214227-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 363cdc04-8630-403e-ac93-f1c7b1a75157)...