0s autopkgtest [21:45:15]: starting date and time: 2024-03-13 21:45:15+0000 0s autopkgtest [21:45:15]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [21:45:15]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f_mbvqzo/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 pycoqc --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-arm64-1.secgroup --name adt-noble-arm64-pycoqc-20240313-214514-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/ 93s autopkgtest [21:46:48]: testbed dpkg architecture: arm64 93s autopkgtest [21:46:48]: testbed apt version: 2.7.12 93s autopkgtest [21:46:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 95s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [450 kB] 95s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2818 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [42.3 kB] 95s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [603 kB] 95s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 95s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [20.3 kB] 95s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 95s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3218 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [42.3 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 97s Fetched 7327 kB in 2s (3901 kB/s) 97s Reading package lists... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Calculating upgrade... 103s The following packages will be REMOVED: 103s libssl3 103s The following NEW packages will be installed: 103s libssl3t64 103s The following packages will be upgraded: 103s console-setup console-setup-linux keyboard-configuration openssl 103s 4 upgraded, 1 newly installed, 1 to remove and 0 not upgraded. 103s Need to get 4955 kB of archives. 103s After this operation, 74.8 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 104s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 104s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup-linux all 1.226ubuntu1 [1880 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 console-setup all 1.226ubuntu1 [110 kB] 105s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 keyboard-configuration all 1.226ubuntu1 [212 kB] 105s Preconfiguring packages ... 106s Fetched 4955 kB in 2s (2420 kB/s) 106s (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.) 106s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 106s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 106s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 106s wget depends on libssl3 (>= 3.0.0). 106s u-boot-tools depends on libssl3 (>= 3.0.0). 106s tnftp depends on libssl3 (>= 3.0.0). 106s tcpdump depends on libssl3 (>= 3.0.0). 106s systemd-resolved depends on libssl3 (>= 3.0.0). 106s systemd depends on libssl3 (>= 3.0.0). 106s sudo depends on libssl3 (>= 3.0.0). 106s sbsigntool depends on libssl3 (>= 3.0.0). 106s rsync depends on libssl3 (>= 3.0.0). 106s python3-cryptography depends on libssl3 (>= 3.0.0). 106s openssh-server depends on libssl3 (>= 3.0.10). 106s openssh-client depends on libssl3 (>= 3.0.10). 106s mtd-utils depends on libssl3 (>= 3.0.0). 106s mokutil depends on libssl3 (>= 3.0.0). 106s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 106s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 106s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 106s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 106s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 106s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 106s libnvme1 depends on libssl3 (>= 3.0.0). 106s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 106s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 106s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 106s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 106s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 106s kmod depends on libssl3 (>= 3.0.0). 106s dhcpcd-base depends on libssl3 (>= 3.0.0). 106s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 106s 107s (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.) 107s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 107s Selecting previously unselected package libssl3t64:arm64. 107s (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.) 107s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 107s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 107s Preparing to unpack .../console-setup-linux_1.226ubuntu1_all.deb ... 107s Unpacking console-setup-linux (1.226ubuntu1) over (1.223ubuntu2) ... 107s Preparing to unpack .../console-setup_1.226ubuntu1_all.deb ... 107s Unpacking console-setup (1.226ubuntu1) over (1.223ubuntu2) ... 107s Preparing to unpack .../keyboard-configuration_1.226ubuntu1_all.deb ... 107s Unpacking keyboard-configuration (1.226ubuntu1) over (1.223ubuntu2) ... 107s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 107s Setting up keyboard-configuration (1.226ubuntu1) ... 108s Your console font configuration will be updated the next time your system 108s boots. If you want to update it now, run 'setupcon' from a virtual console. 108s update-initramfs: deferring update (trigger activated) 108s Setting up openssl (3.0.13-0ubuntu1) ... 108s Setting up console-setup-linux (1.226ubuntu1) ... 110s Setting up console-setup (1.226ubuntu1) ... 111s update-initramfs: deferring update (trigger activated) 111s Processing triggers for man-db (2.12.0-3) ... 112s Processing triggers for libc-bin (2.39-0ubuntu2) ... 113s Processing triggers for initramfs-tools (0.142ubuntu20) ... 113s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic 113s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 137s System running in EFI mode, skipping. 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 140s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 147s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Calculating upgrade... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s autopkgtest [21:47:44]: rebooting testbed after setup commands that affected boot 187s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 195s autopkgtest [21:48:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 197s autopkgtest [21:48:32]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 204s Get:1 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 204s Get:2 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 204s Get:3 http://ftpmaster.internal/ubuntu noble/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 204s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 204s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 204s gpgv: issuer "tille@debian.org" 204s gpgv: Can't check signature: No public key 204s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 206s autopkgtest [21:48:41]: testing package pycoqc version 2.5.2+dfsg-3 206s autopkgtest [21:48:41]: build not needed 210s autopkgtest [21:48:45]: test run-unit-test: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 214s The following additional packages will be installed: 214s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 214s libhts3 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libpython3.11-minimal 214s libpython3.11-stdlib libsz2 pycoqc python3-dateutil python3-decorator 214s python3-fastjsonschema python3-h5py python3-h5py-serial python3-jupyter-core 214s python3-nbformat python3-numpy python3-pandas python3-pandas-lib 214s python3-platformdirs python3-plotly python3-pysam python3-scipy 214s python3-tenacity python3-tqdm python3-traitlets python3.11 214s python3.11-minimal 214s Suggested packages: 214s python-fastjsonschema-doc python-h5py-doc python3-pip gcc gfortran 214s python3-dev python3-pytest python-pandas-doc python3-statsmodels 214s python3-matplotlib ipython3 python3-ipykernel python-scipy-doc 214s python-tenacity-doc python3.11-venv python3.11-doc binfmt-support 214s Recommended packages: 214s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 214s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 214s g++ | c++-compiler python3-pil 215s The following NEW packages will be installed: 215s autopkgtest-satdep libaec0 libblas3 libdeflate0 libgfortran5 215s libhdf5-103-1t64 libhdf5-hl-100t64 libhts3 libhtscodecs2 liblapack3 215s liblbfgsb0 liblzf1 libpython3.11-minimal libpython3.11-stdlib libsz2 pycoqc 215s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 215s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 215s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 215s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 215s python3.11 python3.11-minimal 215s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 51.9 MB/51.9 MB of archives. 215s After this operation, 312 MB of additional disk space will be used. 215s Get:1 /tmp/autopkgtest.eIa2HR/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 215s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 216s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 216s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 216s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 216s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 216s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 216s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 216s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 216s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 216s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu2 [1192 kB] 216s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu2 [55.8 kB] 216s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 216s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 216s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 216s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 216s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 216s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 216s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu2 [887 kB] 216s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 216s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 217s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 217s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 217s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fastjsonschema all 2.19.0-1 [19.6 kB] 217s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-platformdirs all 4.2.0-1 [16.1 kB] 217s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 217s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jupyter-core all 5.3.2-1ubuntu1 [25.5 kB] 217s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 217s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tenacity all 8.2.3-2 [14.8 kB] 217s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-plotly all 5.15.0+dfsg1-1 [2222 kB] 217s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 217s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 217s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-tqdm all 4.64.1-2 [95.2 kB] 217s Get:34 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-h5py all 3.10.0-1ubuntu2 [7980 B] 217s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 pycoqc all 2.5.2+dfsg-3 [36.4 kB] 218s Fetched 51.9 MB in 2s (20.8 MB/s) 219s Selecting previously unselected package libpython3.11-minimal:arm64. 219s (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.) 219s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 219s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 219s Selecting previously unselected package python3.11-minimal. 219s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 219s Unpacking python3.11-minimal (3.11.8-1) ... 219s Selecting previously unselected package libpython3.11-stdlib:arm64. 219s Preparing to unpack .../02-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 219s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 219s Selecting previously unselected package python3.11. 219s Preparing to unpack .../03-python3.11_3.11.8-1_arm64.deb ... 219s Unpacking python3.11 (3.11.8-1) ... 219s Selecting previously unselected package libaec0:arm64. 219s Preparing to unpack .../04-libaec0_1.1.2-1_arm64.deb ... 219s Unpacking libaec0:arm64 (1.1.2-1) ... 219s Selecting previously unselected package libblas3:arm64. 219s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ... 219s Unpacking libblas3:arm64 (3.12.0-3) ... 219s Selecting previously unselected package libdeflate0:arm64. 219s Preparing to unpack .../06-libdeflate0_1.19-1_arm64.deb ... 219s Unpacking libdeflate0:arm64 (1.19-1) ... 219s Selecting previously unselected package libgfortran5:arm64. 220s Preparing to unpack .../07-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 220s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 220s Selecting previously unselected package libsz2:arm64. 220s Preparing to unpack .../08-libsz2_1.1.2-1_arm64.deb ... 220s Unpacking libsz2:arm64 (1.1.2-1) ... 220s Selecting previously unselected package libhdf5-103-1t64:arm64. 220s Preparing to unpack .../09-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 220s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 220s Selecting previously unselected package libhdf5-hl-100t64:arm64. 220s Preparing to unpack .../10-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu2_arm64.deb ... 220s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 220s Selecting previously unselected package libhtscodecs2:arm64. 220s Preparing to unpack .../11-libhtscodecs2_1.6.0-1_arm64.deb ... 220s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 220s Selecting previously unselected package libhts3:arm64. 220s Preparing to unpack .../12-libhts3_1.18+ds-1_arm64.deb ... 220s Unpacking libhts3:arm64 (1.18+ds-1) ... 220s Selecting previously unselected package liblapack3:arm64. 220s Preparing to unpack .../13-liblapack3_3.12.0-3_arm64.deb ... 220s Unpacking liblapack3:arm64 (3.12.0-3) ... 220s Selecting previously unselected package liblbfgsb0:arm64. 220s Preparing to unpack .../14-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 220s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 220s Selecting previously unselected package liblzf1:arm64. 220s Preparing to unpack .../15-liblzf1_3.6-4_arm64.deb ... 220s Unpacking liblzf1:arm64 (3.6-4) ... 220s Selecting previously unselected package python3-numpy. 220s Preparing to unpack .../16-python3-numpy_1%3a1.24.2-2_arm64.deb ... 220s Unpacking python3-numpy (1:1.24.2-2) ... 220s Selecting previously unselected package python3-h5py-serial. 220s Preparing to unpack .../17-python3-h5py-serial_3.10.0-1ubuntu2_arm64.deb ... 220s Unpacking python3-h5py-serial (3.10.0-1ubuntu2) ... 220s Selecting previously unselected package python3-dateutil. 220s Preparing to unpack .../18-python3-dateutil_2.8.2-3_all.deb ... 220s Unpacking python3-dateutil (2.8.2-3) ... 220s Selecting previously unselected package python3-pandas-lib:arm64. 220s Preparing to unpack .../19-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 220s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 221s Selecting previously unselected package python3-pandas. 221s Preparing to unpack .../20-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 221s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 221s Selecting previously unselected package python3-decorator. 221s Preparing to unpack .../21-python3-decorator_5.1.1-5_all.deb ... 221s Unpacking python3-decorator (5.1.1-5) ... 221s Selecting previously unselected package python3-fastjsonschema. 221s Preparing to unpack .../22-python3-fastjsonschema_2.19.0-1_all.deb ... 221s Unpacking python3-fastjsonschema (2.19.0-1) ... 221s Selecting previously unselected package python3-platformdirs. 221s Preparing to unpack .../23-python3-platformdirs_4.2.0-1_all.deb ... 221s Unpacking python3-platformdirs (4.2.0-1) ... 222s Selecting previously unselected package python3-traitlets. 222s Preparing to unpack .../24-python3-traitlets_5.5.0-2_all.deb ... 222s Unpacking python3-traitlets (5.5.0-2) ... 222s Selecting previously unselected package python3-jupyter-core. 222s Preparing to unpack .../25-python3-jupyter-core_5.3.2-1ubuntu1_all.deb ... 222s Unpacking python3-jupyter-core (5.3.2-1ubuntu1) ... 222s Selecting previously unselected package python3-nbformat. 222s Preparing to unpack .../26-python3-nbformat_5.9.1-1_all.deb ... 222s Unpacking python3-nbformat (5.9.1-1) ... 222s Selecting previously unselected package python3-tenacity. 222s Preparing to unpack .../27-python3-tenacity_8.2.3-2_all.deb ... 222s Unpacking python3-tenacity (8.2.3-2) ... 222s Selecting previously unselected package python3-plotly. 222s Preparing to unpack .../28-python3-plotly_5.15.0+dfsg1-1_all.deb ... 222s Unpacking python3-plotly (5.15.0+dfsg1-1) ... 223s Selecting previously unselected package python3-pysam. 223s Preparing to unpack .../29-python3-pysam_0.22.0+ds-1_arm64.deb ... 223s Unpacking python3-pysam (0.22.0+ds-1) ... 223s Selecting previously unselected package python3-scipy. 223s Preparing to unpack .../30-python3-scipy_1.11.4-6_arm64.deb ... 223s Unpacking python3-scipy (1.11.4-6) ... 224s Selecting previously unselected package python3-tqdm. 224s Preparing to unpack .../31-python3-tqdm_4.64.1-2_all.deb ... 224s Unpacking python3-tqdm (4.64.1-2) ... 224s Selecting previously unselected package python3-h5py. 224s Preparing to unpack .../32-python3-h5py_3.10.0-1ubuntu2_all.deb ... 224s Unpacking python3-h5py (3.10.0-1ubuntu2) ... 224s Selecting previously unselected package pycoqc. 224s Preparing to unpack .../33-pycoqc_2.5.2+dfsg-3_all.deb ... 224s Unpacking pycoqc (2.5.2+dfsg-3) ... 224s Selecting previously unselected package autopkgtest-satdep. 224s Preparing to unpack .../34-1-autopkgtest-satdep.deb ... 224s Unpacking autopkgtest-satdep (0) ... 224s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 224s Setting up python3-tenacity (8.2.3-2) ... 224s Setting up python3-tqdm (4.64.1-2) ... 224s Setting up libdeflate0:arm64 (1.19-1) ... 224s Setting up libaec0:arm64 (1.1.2-1) ... 224s Setting up python3-platformdirs (4.2.0-1) ... 224s Setting up python3-decorator (5.1.1-5) ... 224s Setting up libblas3:arm64 (3.12.0-3) ... 224s 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 224s Setting up liblzf1:arm64 (3.6-4) ... 224s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 224s Setting up python3-fastjsonschema (2.19.0-1) ... 224s Setting up python3-traitlets (5.5.0-2) ... 225s Setting up python3-dateutil (2.8.2-3) ... 225s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 225s Setting up python3-jupyter-core (5.3.2-1ubuntu1) ... 225s Setting up libsz2:arm64 (1.1.2-1) ... 225s Setting up python3.11-minimal (3.11.8-1) ... 226s Setting up liblapack3:arm64 (3.12.0-3) ... 226s 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 226s Setting up libhts3:arm64 (1.18+ds-1) ... 226s Setting up python3-pysam (0.22.0+ds-1) ... 226s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 226s Setting up python3-nbformat (5.9.1-1) ... 226s Setting up python3-plotly (5.15.0+dfsg1-1) ... 231s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 231s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 231s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu2) ... 231s Setting up python3.11 (3.11.8-1) ... 232s Setting up python3-numpy (1:1.24.2-2) ... 234s Setting up python3-scipy (1.11.4-6) ... 237s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 237s Setting up python3-h5py-serial (3.10.0-1ubuntu2) ... 237s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 241s Setting up python3-h5py (3.10.0-1ubuntu2) ... 241s Setting up pycoqc (2.5.2+dfsg-3) ... 241s Setting up autopkgtest-satdep (0) ... 241s Processing triggers for systemd (255.2-3ubuntu2) ... 242s Processing triggers for man-db (2.12.0-3) ... 243s Processing triggers for libc-bin (2.39-0ubuntu2) ... 247s (Reading database ... 94263 files and directories currently installed.) 247s Removing autopkgtest-satdep (0) ... 247s autopkgtest [21:49:22]: test run-unit-test: [----------------------- 248s Test 1 249s Checking arguments values 249s Check input data files 249s Parse data files 249s Merge data 249s Cleaning data 249s Loading plotting interface 250s PASS 250s 250s Test 2 251s Checking arguments values 251s Check input data files 251s Parse data files 251s Merge data 251s Cleaning data 251s Loading plotting interface 252s PASS 252s 252s Test 3 253s Checking arguments values 253s Check input data files 253s Parse data files 253s Merge data 253s Cleaning data 253s Loading plotting interface 254s PASS 254s 254s Test 4 255s Checking arguments values 255s Check input data files 255s Parse data files 255s Merge data 255s Cleaning data 255s Loading plotting interface 256s PASS 256s 256s Test 5 257s Checking arguments values 257s Check input data files 257s Parse data files 258s Merge data 258s Cleaning data 258s Loading plotting interface 259s PASS 259s 259s Test 6 260s PASS 260s 260s Test 7 261s Checking arguments values 261s Check input data files 261s Parse data files 261s Merge data 261s Cleaning data 261s Loading plotting interface 262s PASS 262s 262s Test 8 263s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2158.78 reads/s] 263s Total reads: 22 / Average speed: 587.54 reads/s 263s 263s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 263s 3784283c-47cc-48ac-8d7b-7efd32123b56 40ebe55356ada6c830fa793745ef4c498d896c73 243 20 893 8.54 filtered_out 263s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out 263s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 263s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 263s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 263s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 263s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out 263s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 263s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 263s PASS 263s 263s Test 9 263s Check input data and options 263s Start processing fast5 files 263s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1088.17 reads/s] 263s Overall counts valid files: 22 263s 263s fields found mean_qscore_template: 22 263s called_events: 22 263s duration: 22 263s strand_score: 22 263s 263s fields not found 263s Total reads: 22 / Average speed: 599.48 reads/s 263s 264s mean_qscore_template called_events duration strand_score 264s 8.741 3117 46767 -0.0006 264s 7.608 1615 24233 -0.0007 264s 7.742 2142 32138 -0.0004 264s 8.54 2023 30405 -0.0003 264s 8.304 1547 23218 -0.0008 264s 7.805 1438 21583 -0.0006 264s 7.881 1513 24541 -0.0007 264s 8.234 1827 27409 -0.0011 264s 8.987 4235 63526 -0.0003 264s PASS 264s 264s Test 10 264s Check input data and options 264s Start processing fast5 files 264s 0 reads [00:00, ? reads/s] 22 reads [00:00, 2154.14 reads/s] 264s Overall counts valid files: 22 264s 264s fields found read_id: 22 264s run_id: 22 264s channel: 22 264s start_time: 22 264s sequence_length_template: 22 264s mean_qscore_template: 22 264s calibration_strand_genome_template: 22 264s 264s fields not found barcode_arrangement: 22 264s 264s Total reads: 22 / Average speed: 130.65 reads/s 264s 265s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 265s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_290_strand.fast5 265s 3784283c-47cc-48ac-8d7b-7efd32123b56 40ebe55356ada6c830fa793745ef4c498d896c73 243 20 893 8.54 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_243_strand.fast5 265s 5b7fadd0-c646-4c7b-9800-66ee658a5ca8 40ebe55356ada6c830fa793745ef4c498d896c73 150 37 468 7.608 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_150_strand.fast5 265s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 265s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_36_strand.fast5 265s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 265s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 265s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_418_strand.fast5 265s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.eIa2HR/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 265s PASS 265s 265s Test 11 265s Import data from sequencing summary file(s) and cleanup 265s Read files and import in a dataframe 265s Check input data files 265s Parse data files 266s Merge data 266s Cleanup missing barcodes values 266s Cleaning up low frequency barcodes 266s Split data per barcode 266s Processing data for Barcode barcode02 266s Processing data for Barcode barcode07 266s Processing data for Barcode barcode08 266s Processing data for Barcode barcode09 266s Processing data for Barcode barcode10 267s Processing data for Barcode barcode11 267s Processing data for Barcode barcode12 267s Processing data for Barcode unclassified 267s Barcode Counts 267s Counts Write 267s barcode02 2 False 267s barcode07 1 False 267s barcode08 30 False 267s barcode09 9945 True 267s barcode10 12644 True 267s barcode11 13594 True 267s barcode12 9813 True 267s unclassified 3971 False 267s PASS 267s 267s Test 12 268s General info 268s package_name: pycoQC 268s package_version: 2.5.2 268s timestamp: 2024-03-13 21:49:43.457485 268s 268s Runtime options 268s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 268s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 268s output_dir: results/ 268s output_unclassified: False 268s min_barcode_percent: 0.1 268s verbose: True 268s quiet: False 268s 268s Import data from sequencing summary file(s) and cleanup 268s Read files and import in a dataframe 268s Check input data files 268s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 268s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 268s Parse data files 268s Parse summary files 268s 3,999 reads found in initial file 268s Parse barcode files 268s Found valid Deepbinner barcode file 268s 3,775 reads with barcodes assigned 268s Merge data 268s Cleanup missing barcodes values 268s Cleaning up low frequency barcodes 268s Split data per barcode 268s Processing data for Barcode 1 268s Processing data for Barcode 2 268s Processing data for Barcode 3 268s Processing data for Barcode 4 268s Processing data for Barcode 5 268s Processing data for Barcode 6 268s Processing data for Barcode 7 268s Processing data for Barcode 8 268s Processing data for Barcode unclassified 268s Barcode Counts 268s Counts Write 268s 1 534 True 268s 2 206 True 268s 3 562 True 268s 4 579 True 268s 5 590 True 268s 6 655 True 268s 7 271 True 268s 8 378 True 268s unclassified 224 False 272s PASS 272s 272s Check if files really exist 272s PASS 272s 272s autopkgtest [21:49:45]: test run-unit-test: -----------------------] 272s autopkgtest [21:49:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 272s run-unit-test PASS 272s autopkgtest [21:49:47]: @@@@@@@@@@@@@@@@@@@@ summary 272s run-unit-test PASS 277s Creating nova instance adt-noble-arm64-pycoqc-20240313-214514-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240313.img (UUID 363cdc04-8630-403e-ac93-f1c7b1a75157)...