0s autopkgtest [23:11:45]: starting date and time: 2025-01-03 23:11:45+0000 0s autopkgtest [23:11:45]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:11:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bdsyufxp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade pycoqc --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.13.1-1~exp2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-10.secgroup --name adt-plucky-ppc64el-pycoqc-20250103-231145-juju-7f2275-prod-proposed-migration-environment-2-70b72b59-8656-4ba1-b3f8-cd93b890be3b --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 182s autopkgtest [23:14:47]: testbed dpkg architecture: ppc64el 182s autopkgtest [23:14:47]: testbed apt version: 2.9.18 183s autopkgtest [23:14:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 183s autopkgtest [23:14:48]: testbed release detected to be: None 184s autopkgtest [23:14:49]: updating testbed package index (apt update) 184s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 184s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 184s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 184s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 184s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.5 kB] 184s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [804 kB] 185s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [12.3 kB] 185s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 185s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [87.2 kB] 185s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [756 B] 185s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [693 kB] 185s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [4084 B] 185s Fetched 1763 kB in 1s (1781 kB/s) 186s Reading package lists... 186s Reading package lists... 186s Building dependency tree... 186s Reading state information... 187s Calculating upgrade... 187s The following packages will be upgraded: 187s binutils binutils-common binutils-powerpc64le-linux-gnu libbinutils 187s libctf-nobfd0 libctf0 libsframe1 187s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s Need to get 3752 kB of archives. 187s After this operation, 0 B of additional disk space will be used. 187s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libctf0 ppc64el 2.43.50.20241230-1ubuntu1 [114 kB] 187s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libctf-nobfd0 ppc64el 2.43.50.20241230-1ubuntu1 [117 kB] 187s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.43.50.20241230-1ubuntu1 [2569 kB] 187s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbinutils ppc64el 2.43.50.20241230-1ubuntu1 [711 kB] 187s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el binutils ppc64el 2.43.50.20241230-1ubuntu1 [3096 B] 187s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el binutils-common ppc64el 2.43.50.20241230-1ubuntu1 [222 kB] 188s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsframe1 ppc64el 2.43.50.20241230-1ubuntu1 [15.9 kB] 188s Fetched 3752 kB in 1s (4809 kB/s) 188s (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 ... 74025 files and directories currently installed.) 188s Preparing to unpack .../0-libctf0_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking libctf0:ppc64el (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../1-libctf-nobfd0_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking libctf-nobfd0:ppc64el (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../2-binutils-powerpc64le-linux-gnu_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking binutils-powerpc64le-linux-gnu (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../3-libbinutils_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking libbinutils:ppc64el (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../4-binutils_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking binutils (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../5-binutils-common_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking binutils-common:ppc64el (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Preparing to unpack .../6-libsframe1_2.43.50.20241230-1ubuntu1_ppc64el.deb ... 188s Unpacking libsframe1:ppc64el (2.43.50.20241230-1ubuntu1) over (2.43.50.20241221-1ubuntu1) ... 188s Setting up binutils-common:ppc64el (2.43.50.20241230-1ubuntu1) ... 188s Setting up libctf-nobfd0:ppc64el (2.43.50.20241230-1ubuntu1) ... 188s Setting up libsframe1:ppc64el (2.43.50.20241230-1ubuntu1) ... 188s Setting up libbinutils:ppc64el (2.43.50.20241230-1ubuntu1) ... 188s Setting up libctf0:ppc64el (2.43.50.20241230-1ubuntu1) ... 188s Setting up binutils-powerpc64le-linux-gnu (2.43.50.20241230-1ubuntu1) ... 188s Setting up binutils (2.43.50.20241230-1ubuntu1) ... 188s Processing triggers for libc-bin (2.40-4ubuntu1) ... 188s Processing triggers for man-db (2.13.0-1) ... 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 190s autopkgtest [23:14:55]: upgrading testbed (apt dist-upgrade and autopurge) 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 191s Entering ResolveByKeep 191s 191s The following packages were automatically installed and are no longer required: 191s python3.12 python3.12-minimal 191s Use 'sudo apt autoremove' to remove them. 191s The following NEW packages will be installed: 191s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 191s The following packages will be upgraded: 191s libpython3-stdlib python3 python3-minimal 191s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 6300 kB of archives. 191s After this operation, 26.2 MB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.1-2 [883 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.1-2 [2496 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.13.1-1~exp2 [27.6 kB] 192s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.13.1-1~exp2 [24.0 kB] 192s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.1-2 [2131 kB] 192s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.1-2 [729 kB] 192s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.13.1-1~exp2 [10.2 kB] 192s Fetched 6300 kB in 1s (7741 kB/s) 192s Selecting previously unselected package libpython3.13-minimal:ppc64el. 192s (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 ... 74025 files and directories currently installed.) 192s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_ppc64el.deb ... 192s Unpacking libpython3.13-minimal:ppc64el (3.13.1-2) ... 192s Selecting previously unselected package python3.13-minimal. 192s Preparing to unpack .../python3.13-minimal_3.13.1-2_ppc64el.deb ... 192s Unpacking python3.13-minimal (3.13.1-2) ... 192s Setting up libpython3.13-minimal:ppc64el (3.13.1-2) ... 192s Setting up python3.13-minimal (3.13.1-2) ... 193s (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 ... 74345 files and directories currently installed.) 193s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_ppc64el.deb ... 193s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 193s Setting up python3-minimal (3.13.1-1~exp2) ... 193s (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 ... 74345 files and directories currently installed.) 193s Preparing to unpack .../python3_3.13.1-1~exp2_ppc64el.deb ... 193s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 193s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 193s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_ppc64el.deb ... 193s Unpacking libpython3.13-stdlib:ppc64el (3.13.1-2) ... 193s Selecting previously unselected package python3.13. 193s Preparing to unpack .../python3.13_3.13.1-2_ppc64el.deb ... 193s Unpacking python3.13 (3.13.1-2) ... 193s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_ppc64el.deb ... 193s Unpacking libpython3-stdlib:ppc64el (3.13.1-1~exp2) over (3.12.8-1) ... 193s Setting up libpython3.13-stdlib:ppc64el (3.13.1-2) ... 193s Setting up libpython3-stdlib:ppc64el (3.13.1-1~exp2) ... 193s Setting up python3.13 (3.13.1-2) ... 194s Setting up python3 (3.13.1-1~exp2) ... 194s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 194s for fn in glob1(directory, "%s.*" % fname): 195s Processing triggers for man-db (2.13.0-1) ... 195s Processing triggers for systemd (257-2ubuntu1) ... 195s Reading package lists... 196s Building dependency tree... 196s Reading state information... 196s Starting pkgProblemResolver with broken count: 0 196s Starting 2 pkgProblemResolver with broken count: 0 196s Done 196s The following packages will be REMOVED: 196s python3.12* python3.12-minimal* 197s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 197s After this operation, 9889 kB disk space will be freed. 197s (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 ... 74762 files and directories currently installed.) 197s Removing python3.12 (3.12.8-3) ... 197s Removing python3.12-minimal (3.12.8-3) ... 197s /usr/bin/py3clean:125: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 197s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 197s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for systemd (257-2ubuntu1) ... 198s (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 ... 74734 files and directories currently installed.) 198s Purging configuration files for python3.12-minimal (3.12.8-3) ... 200s autopkgtest [23:15:05]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 201s autopkgtest [23:15:06]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky/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 [23:15:11]: testing package pycoqc version 2.5.2+dfsg-3 207s autopkgtest [23:15:12]: build not needed 211s autopkgtest [23:15:16]: test run-unit-test: preparing testbed 211s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 212s The following NEW packages will be installed: 212s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 212s libhts3t64 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 212s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 212s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 212s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 212s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 212s python3-tz 212s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 53.2 MB of archives. 212s After this operation, 380 MB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-4 [222 kB] 212s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 212s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-12ubuntu1 [571 kB] 213s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 213s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-5ubuntu1 [1394 kB] 213s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-5ubuntu1 [71.2 kB] 213s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 213s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 213s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-4 [2814 kB] 213s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 213s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 213s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-12 [4917 kB] 213s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-8ubuntu3 [1598 kB] 213s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 213s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.2-1 [31.5 kB] 213s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5ubuntu1 [7350 kB] 213s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 213s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 213s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fastjsonschema all 2.21.1-1 [20.4 kB] 213s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-platformdirs all 4.3.6-1 [16.8 kB] 213s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 213s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-jupyter-core all 5.7.2-5 [28.1 kB] 213s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-nbformat all 5.9.1-1 [41.2 kB] 213s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tenacity all 8.5.0-0ubuntu1 [17.0 kB] 213s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-plotly all 5.20.0+dfsg-1 [2766 kB] 213s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2build1 [4445 kB] 213s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.14.1-3ubuntu1 [22.6 MB] 214s Get:29 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.1-1 [92.5 kB] 214s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-8ubuntu3 [7982 B] 214s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pycoqc all 2.5.2+dfsg-3 [36.4 kB] 214s Fetched 53.2 MB in 2s (29.3 MB/s) 214s Selecting previously unselected package libaec0:ppc64el. 214s (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 ... 74734 files and directories currently installed.) 214s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 214s Unpacking libaec0:ppc64el (1.1.3-1) ... 214s Selecting previously unselected package libblas3:ppc64el. 214s Preparing to unpack .../01-libblas3_3.12.0-4_ppc64el.deb ... 214s Unpacking libblas3:ppc64el (3.12.0-4) ... 214s Selecting previously unselected package libdeflate0:ppc64el. 214s Preparing to unpack .../02-libdeflate0_1.22-1_ppc64el.deb ... 214s Unpacking libdeflate0:ppc64el (1.22-1) ... 214s Selecting previously unselected package libgfortran5:ppc64el. 214s Preparing to unpack .../03-libgfortran5_14.2.0-12ubuntu1_ppc64el.deb ... 214s Unpacking libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 214s Selecting previously unselected package libsz2:ppc64el. 214s Preparing to unpack .../04-libsz2_1.1.3-1_ppc64el.deb ... 214s Unpacking libsz2:ppc64el (1.1.3-1) ... 214s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 214s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 214s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 214s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 214s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_ppc64el.deb ... 214s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 214s Selecting previously unselected package libhtscodecs2:ppc64el. 214s 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Unpacking python3-numpy (1:1.26.4+ds-12) ... 215s Selecting previously unselected package python3-h5py-serial. 215s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_ppc64el.deb ... 215s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 215s Selecting previously unselected package python3-dateutil. 215s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 215s Unpacking python3-dateutil (2.9.0-3) ... 215s Selecting previously unselected package python3-tz. 215s Preparing to unpack .../15-python3-tz_2024.2-1_all.deb ... 215s Unpacking python3-tz (2024.2-1) ... 215s Selecting previously unselected package python3-pandas-lib:ppc64el. 215s Preparing to unpack .../16-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_ppc64el.deb ... 215s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 215s Selecting previously unselected package python3-pandas. 215s Preparing to unpack .../17-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 215s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 215s Selecting previously unselected package python3-decorator. 215s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 215s Unpacking python3-decorator (5.1.1-5) ... 215s Selecting previously unselected package python3-fastjsonschema. 215s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 215s Unpacking python3-fastjsonschema (2.21.1-1) ... 215s Selecting previously unselected package python3-platformdirs. 215s Preparing to unpack .../20-python3-platformdirs_4.3.6-1_all.deb ... 215s Unpacking python3-platformdirs (4.3.6-1) ... 215s Selecting previously unselected package python3-traitlets. 215s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 215s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 215s Selecting previously unselected package python3-jupyter-core. 215s Preparing to unpack .../22-python3-jupyter-core_5.7.2-5_all.deb ... 215s Unpacking python3-jupyter-core (5.7.2-5) ... 215s 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Preparing to unpack .../28-python3-tqdm_4.67.1-1_all.deb ... 218s Unpacking python3-tqdm (4.67.1-1) ... 218s Selecting previously unselected package python3-h5py. 218s Preparing to unpack .../29-python3-h5py_3.11.0-8ubuntu3_all.deb ... 218s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 218s Selecting previously unselected package pycoqc. 218s Preparing to unpack .../30-pycoqc_2.5.2+dfsg-3_all.deb ... 218s Unpacking pycoqc (2.5.2+dfsg-3) ... 218s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 218s Setting up python3-tenacity (8.5.0-0ubuntu1) ... 218s Setting up python3-tqdm (4.67.1-1) ... 218s Setting up libdeflate0:ppc64el (1.22-1) ... 218s Setting up libaec0:ppc64el (1.1.3-1) ... 218s Setting up python3-platformdirs (4.3.6-1) ... 218s Setting up python3-tz (2024.2-1) ... 218s Setting up python3-decorator (5.1.1-5) ... 218s Setting up libblas3:ppc64el (3.12.0-4) ... 219s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 219s Setting up liblzf1:ppc64el (3.6-4) ... 219s Setting up libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 219s Setting up python3-fastjsonschema (2.21.1-1) ... 219s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 219s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 219s Setting up python3-dateutil (2.9.0-3) ... 219s Setting up python3-jupyter-core (5.7.2-5) ... 219s Setting up libsz2:ppc64el (1.1.3-1) ... 219s Setting up liblapack3:ppc64el (3.12.0-4) ... 219s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 219s Setting up python3-pysam (0.22.1+ds-2build1) ... 219s Setting up python3-nbformat (5.9.1-1) ... 219s Setting up python3-plotly (5.20.0+dfsg-1) ... 226s Setting up python3-numpy (1:1.26.4+ds-12) ... 227s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-5ubuntu1) ... 227s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 228s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-5ubuntu1) ... 228s Setting up python3-scipy (1.14.1-3ubuntu1) ... 231s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 231s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 231s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 236s Setting up python3-h5py (3.11.0-8ubuntu3) ... 236s Setting up pycoqc (2.5.2+dfsg-3) ... 236s Processing triggers for libc-bin (2.40-4ubuntu1) ... 236s Processing triggers for man-db (2.13.0-1) ... 237s autopkgtest [23:15:42]: test run-unit-test: [----------------------- 238s Test 1 239s Checking arguments values 239s Check input data files 239s Parse data files 239s Merge data 239s Cleaning data 239s Loading plotting interface 240s PASS 240s 240s Test 2 240s Checking arguments values 240s Check input data files 240s Parse data files 241s Merge data 241s Cleaning data 241s Loading plotting interface 241s PASS 241s 241s Test 3 242s Checking arguments values 242s Check input data files 242s Parse data files 242s Merge data 242s Cleaning data 242s Loading plotting interface 243s PASS 243s 243s Test 4 243s Checking arguments values 243s Check input data files 243s Parse data files 244s Merge data 244s Cleaning data 244s Loading plotting interface 244s PASS 244s 244s Test 5 245s Checking arguments values 245s Check input data files 245s Parse data files 245s Merge data 245s Cleaning data 245s Loading plotting interface 246s PASS 246s 246s Test 6 247s PASS 247s 247s Test 7 247s Checking arguments values 247s Check input data files 247s Parse data files 247s Merge data 247s Cleaning data 247s Loading plotting interface 248s PASS 248s 248s Test 8 249s 0 reads [00:00, ? reads/s] 22 reads [00:00, 846.97 reads/s] 249s Total reads: 22 / Average speed: 587.02 reads/s 249s 249s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 249s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out 249s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 249s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out 249s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 249s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out 249s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 249s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out 249s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out 249s 4e21bf07-e2df-42d8-b347-59ef2c0618ea 40ebe55356ada6c830fa793745ef4c498d896c73 290 31 1160 8.741 filtered_out 249s PASS 249s 249s Test 9 250s Check input data and options 250s Start processing fast5 files 250s 0 reads [00:00, ? reads/s] 22 reads [00:00, 1316.31 reads/s] 250s Overall counts valid files: 22 250s 250s fields found mean_qscore_template: 22 250s called_events: 22 250s duration: 22 250s strand_score: 22 250s 250s fields not found 250s Total reads: 22 / Average speed: 859.07 reads/s 250s 250s mean_qscore_template called_events duration strand_score 250s 7.805 1438 21583 -0.0006 250s 9.407 2848 42730 -0.0003 250s 8.304 1547 23218 -0.0008 250s 7.881 1513 24541 -0.0007 250s 8.56 5838 87570 -0.0003 250s 8.23 2778 51387 -0.0007 250s 8.693 2383 35752 -0.0005 250s 8.206 1649 24747 -0.0009 250s 8.124 2978 44675 -0.0005 250s PASS 250s 250s Test 10 250s Check input data and options 250s Start processing fast5 files 251s 0 reads [00:00, ? reads/s] 22 reads [00:00, 959.43 reads/s] 251s Overall counts valid files: 22 251s 251s fields found read_id: 22 251s run_id: 22 251s channel: 22 251s start_time: 22 251s sequence_length_template: 22 251s mean_qscore_template: 22 251s calibration_strand_genome_template: 22 251s 251s fields not found barcode_arrangement: 22 251s 251s Total reads: 22 / Average speed: 694.66 reads/s 251s 251s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 251s 08642be5-5cf7-4c4c-8c45-e4d569b9a482 40ebe55356ada6c830fa793745ef4c498d896c73 121 28 450 7.805 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_121_strand.fast5 251s 61e799eb-5571-4cc4-bbf6-b3929b197459 40ebe55356ada6c830fa793745ef4c498d896c73 103 26 844 8.56 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_103_strand.fast5 251s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 251s c38cbad9-d91e-4208-9317-832f4e2cc289 40ebe55356ada6c830fa793745ef4c498d896c73 113 30 824 8.693 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_113_strand.fast5 251s f8325de9-a77e-4616-a4a8-69ecf32e1688 40ebe55356ada6c830fa793745ef4c498d896c73 354 16 568 8.206 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_354_strand.fast5 251s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_348_strand.fast5 251s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 251s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 251s 6f4fffe7-ca07-4c5e-9ad1-7470f370a8b0 40ebe55356ada6c830fa793745ef4c498d896c73 301 16 553 7.881 filtered_out /tmp/autopkgtest.itfhjG/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_301_strand.fast5 251s PASS 251s 251s Test 11 251s Import data from sequencing summary file(s) and cleanup 251s Read files and import in a dataframe 251s Check input data files 251s Parse data files 252s Merge data 252s Cleanup missing barcodes values 252s Cleaning up low frequency barcodes 252s Split data per barcode 252s Processing data for Barcode barcode02 252s Processing data for Barcode barcode07 252s Processing data for Barcode barcode08 252s Processing data for Barcode barcode09 252s Processing data for Barcode barcode10 252s Processing data for Barcode barcode11 252s Processing data for Barcode barcode12 252s Processing data for Barcode unclassified 252s Barcode Counts 252s Counts Write 252s barcode02 2 False 252s barcode07 1 False 252s barcode08 30 False 252s barcode09 9945 True 252s barcode10 12644 True 252s barcode11 13594 True 252s barcode12 9813 True 252s unclassified 3971 False 252s PASS 252s 252s Test 12 253s General info 253s package_name: pycoQC 253s package_version: 2.5.2 253s timestamp: 2025-01-03 23:15:58.528321 253s 253s Runtime options 253s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 253s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 253s output_dir: results/ 253s output_unclassified: False 253s min_barcode_percent: 0.1 253s verbose: True 253s quiet: False 253s 253s Import data from sequencing summary file(s) and cleanup 253s Read files and import in a dataframe 253s Check input data files 253s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 253s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 253s Parse data files 253s Parse summary files 253s 3,999 reads found in initial file 253s Parse barcode files 253s Found valid Deepbinner barcode file 253s 3,775 reads with barcodes assigned 253s Merge data 253s Cleanup missing barcodes values 253s Cleaning up low frequency barcodes 253s Split data per barcode 253s Processing data for Barcode 1 253s Processing data for Barcode 2 253s Processing data for Barcode 3 253s Processing data for Barcode 4 253s Processing data for Barcode 5 253s Processing data for Barcode 6 253s Processing data for Barcode 7 253s Processing data for Barcode 8 253s Processing data for Barcode unclassified 253s Barcode Counts 253s Counts Write 253s 1 534 True 253s 2 206 True 253s 3 562 True 253s 4 579 True 253s 5 590 True 253s 6 655 True 253s 7 271 True 253s 8 378 True 253s unclassified 224 False 253s PASS 253s 253s Check if files really exist 253s PASS 253s 254s autopkgtest [23:15:59]: test run-unit-test: -----------------------] 254s run-unit-test PASS 254s autopkgtest [23:15:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 254s autopkgtest [23:15:59]: @@@@@@@@@@@@@@@@@@@@ summary 254s run-unit-test PASS 259s nova [W] Using flock in prodstack6-ppc64el 259s Creating nova instance adt-plucky-ppc64el-pycoqc-20250103-231145-juju-7f2275-prod-proposed-migration-environment-2-70b72b59-8656-4ba1-b3f8-cd93b890be3b from image adt/ubuntu-plucky-ppc64el-server-20250103.img (UUID f20efbba-1df4-424c-8de8-0f24e2643aa4)... 259s nova [W] Timed out waiting for 5eebd49d-6219-49d5-8bd9-c8bc320a4355 to get deleted.