0s autopkgtest [14:02:30]: starting date and time: 2025-01-03 14:02:30+0000 0s autopkgtest [14:02:30]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:02:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sg_sqrrr/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-36.secgroup --name adt-plucky-arm64-pycoqc-20250103-140230-juju-7f2275-prod-proposed-migration-environment-2-fae6503b-bb0e-447d-aa77-96c8b7411356 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 189s autopkgtest [14:05:39]: testbed dpkg architecture: arm64 189s autopkgtest [14:05:39]: testbed apt version: 2.9.18 190s autopkgtest [14:05:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 190s autopkgtest [14:05:40]: testbed release detected to be: None 191s autopkgtest [14:05:41]: updating testbed package index (apt update) 191s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 191s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 191s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 191s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 191s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [10.1 kB] 191s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 191s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [60.7 kB] 191s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [664 kB] 192s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [86.7 kB] 192s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 192s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [561 kB] 192s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [8824 B] 192s Fetched 1533 kB in 1s (1703 kB/s) 193s Reading package lists... 193s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Calculating upgrade... 195s The following packages will be upgraded: 195s base-passwd bash-completion 195s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 195s Need to get 267 kB of archives. 195s After this operation, 143 kB of additional disk space will be used. 195s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 base-passwd arm64 3.6.6 [53.6 kB] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 bash-completion all 1:2.16.0-1 [214 kB] 196s Preconfiguring packages ... 196s Fetched 267 kB in 0s (566 kB/s) 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 ... 80060 files and directories currently installed.) 197s Preparing to unpack .../base-passwd_3.6.6_arm64.deb ... 197s Unpacking base-passwd (3.6.6) over (3.6.5) ... 197s Setting up base-passwd (3.6.6) ... 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 ... 80060 files and directories currently installed.) 197s Preparing to unpack .../bash-completion_1%3a2.16.0-1_all.deb ... 197s Unpacking bash-completion (1:2.16.0-1) over (1:2.14.0-2) ... 197s Setting up bash-completion (1:2.16.0-1) ... 197s Processing triggers for man-db (2.13.0-1) ... 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 201s autopkgtest [14:05:51]: upgrading testbed (apt dist-upgrade and autopurge) 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 202s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 203s Entering ResolveByKeep 203s 204s The following packages were automatically installed and are no longer required: 204s python3.12 python3.12-minimal 204s Use 'sudo apt autoremove' to remove them. 204s The following NEW packages will be installed: 204s libpython3.13-minimal libpython3.13-stdlib python3.13 python3.13-minimal 204s The following packages will be upgraded: 204s libpython3-stdlib python3 python3-minimal 204s 3 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 204s Need to get 5992 kB of archives. 204s After this operation, 24.3 MB of additional disk space will be used. 204s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.1-2 [879 kB] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.1-2 [2262 kB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.13.1-1~exp2 [27.6 kB] 204s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.13.1-1~exp2 [23.9 kB] 204s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.1-2 [2061 kB] 205s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.1-2 [729 kB] 205s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.13.1-1~exp2 [10.2 kB] 205s Fetched 5992 kB in 1s (7738 kB/s) 205s Selecting previously unselected package libpython3.13-minimal:arm64. 205s (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 ... 80185 files and directories currently installed.) 205s Preparing to unpack .../libpython3.13-minimal_3.13.1-2_arm64.deb ... 205s Unpacking libpython3.13-minimal:arm64 (3.13.1-2) ... 205s Selecting previously unselected package python3.13-minimal. 205s Preparing to unpack .../python3.13-minimal_3.13.1-2_arm64.deb ... 205s Unpacking python3.13-minimal (3.13.1-2) ... 205s Setting up libpython3.13-minimal:arm64 (3.13.1-2) ... 205s Setting up python3.13-minimal (3.13.1-2) ... 207s (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 ... 80505 files and directories currently installed.) 207s Preparing to unpack .../python3-minimal_3.13.1-1~exp2_arm64.deb ... 207s Unpacking python3-minimal (3.13.1-1~exp2) over (3.12.8-1) ... 207s Setting up python3-minimal (3.13.1-1~exp2) ... 208s (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 ... 80505 files and directories currently installed.) 208s Preparing to unpack .../python3_3.13.1-1~exp2_arm64.deb ... 208s Unpacking python3 (3.13.1-1~exp2) over (3.12.8-1) ... 208s Selecting previously unselected package libpython3.13-stdlib:arm64. 208s Preparing to unpack .../libpython3.13-stdlib_3.13.1-2_arm64.deb ... 208s Unpacking libpython3.13-stdlib:arm64 (3.13.1-2) ... 208s Selecting previously unselected package python3.13. 208s Preparing to unpack .../python3.13_3.13.1-2_arm64.deb ... 208s Unpacking python3.13 (3.13.1-2) ... 208s Preparing to unpack .../libpython3-stdlib_3.13.1-1~exp2_arm64.deb ... 208s Unpacking libpython3-stdlib:arm64 (3.13.1-1~exp2) over (3.12.8-1) ... 208s Setting up libpython3.13-stdlib:arm64 (3.13.1-2) ... 208s Setting up libpython3-stdlib:arm64 (3.13.1-1~exp2) ... 208s Setting up python3.13 (3.13.1-2) ... 210s Setting up python3 (3.13.1-1~exp2) ... 210s /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. 210s for fn in glob1(directory, "%s.*" % fname): 210s Processing triggers for man-db (2.13.0-1) ... 211s Processing triggers for systemd (257-2ubuntu1) ... 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 213s The following packages will be REMOVED: 213s python3.12* python3.12-minimal* 213s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 213s After this operation, 8710 kB disk space will be freed. 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 ... 80922 files and directories currently installed.) 214s Removing python3.12 (3.12.8-3) ... 214s Removing python3.12-minimal (3.12.8-3) ... 214s /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. 214s for fn in glob1(directory, "%s.%s.py[co]" % (fname, magic_tag)): 215s Processing triggers for man-db (2.13.0-1) ... 215s Processing triggers for systemd (257-2ubuntu1) ... 215s (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 ... 80894 files and directories currently installed.) 215s Purging configuration files for python3.12-minimal (3.12.8-3) ... 218s autopkgtest [14:06:08]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 219s autopkgtest [14:06:09]: @@@@@@@@@@@@@@@@@@@@ apt-source pycoqc 222s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (dsc) [2051 B] 222s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (tar) [41.6 MB] 222s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pycoqc 2.5.2+dfsg-3 (diff) [6764 B] 222s gpgv: Signature made Tue Dec 7 15:51:27 2021 UTC 222s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 222s gpgv: issuer "tille@debian.org" 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./pycoqc_2.5.2+dfsg-3.dsc: no acceptable signature found 224s autopkgtest [14:06:14]: testing package pycoqc version 2.5.2+dfsg-3 225s autopkgtest [14:06:15]: build not needed 229s autopkgtest [14:06:19]: test run-unit-test: preparing testbed 229s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s Starting pkgProblemResolver with broken count: 0 230s Starting 2 pkgProblemResolver with broken count: 0 230s Done 231s The following NEW packages will be installed: 231s libaec0 libblas3 libdeflate0 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 231s libhts3t64 libhtscodecs2 liblapack3 liblbfgsb0 liblzf1 libsz2 pycoqc 231s python3-dateutil python3-decorator python3-fastjsonschema python3-h5py 231s python3-h5py-serial python3-jupyter-core python3-nbformat python3-numpy 231s python3-pandas python3-pandas-lib python3-platformdirs python3-plotly 231s python3-pysam python3-scipy python3-tenacity python3-tqdm python3-traitlets 231s python3-tz 231s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 47.1 MB of archives. 231s After this operation, 312 MB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 232s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 232s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 232s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-12ubuntu1 [437 kB] 232s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 232s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-5ubuntu1 [1210 kB] 232s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-5ubuntu1 [56.9 kB] 232s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 232s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 232s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 232s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 232s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 232s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [4153 kB] 232s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 232s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 232s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.2-1 [31.5 kB] 232s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB] 232s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 233s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 233s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fastjsonschema all 2.21.1-1 [20.4 kB] 233s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 233s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-traitlets all 5.14.3+really5.14.3-1 [71.5 kB] 233s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-jupyter-core all 5.7.2-5 [28.1 kB] 233s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-nbformat all 5.9.1-1 [41.2 kB] 233s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tenacity all 8.5.0-0ubuntu1 [17.0 kB] 233s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-plotly all 5.20.0+dfsg-1 [2766 kB] 233s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2build1 [3987 kB] 233s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-3ubuntu1 [19.5 MB] 233s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-1 [92.5 kB] 233s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 233s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 pycoqc all 2.5.2+dfsg-3 [36.4 kB] 234s Fetched 47.1 MB in 2s (25.3 MB/s) 234s Selecting previously unselected package libaec0:arm64. 234s (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 ... 80894 files and directories currently installed.) 234s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 234s Unpacking libaec0:arm64 (1.1.3-1) ... 234s Selecting previously unselected package libblas3:arm64. 234s Preparing to unpack .../01-libblas3_3.12.0-4_arm64.deb ... 234s Unpacking libblas3:arm64 (3.12.0-4) ... 234s Selecting previously unselected package libdeflate0:arm64. 234s Preparing to unpack .../02-libdeflate0_1.22-1_arm64.deb ... 234s Unpacking libdeflate0:arm64 (1.22-1) ... 234s Selecting previously unselected package libgfortran5:arm64. 234s Preparing to unpack .../03-libgfortran5_14.2.0-12ubuntu1_arm64.deb ... 234s Unpacking libgfortran5:arm64 (14.2.0-12ubuntu1) ... 234s Selecting previously unselected package libsz2:arm64. 234s Preparing to unpack .../04-libsz2_1.1.3-1_arm64.deb ... 234s Unpacking libsz2:arm64 (1.1.3-1) ... 234s Selecting previously unselected package libhdf5-103-1t64:arm64. 234s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_arm64.deb ... 234s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 234s Selecting previously unselected package libhdf5-hl-100t64:arm64. 234s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-5ubuntu1_arm64.deb ... 234s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 234s Selecting previously unselected package libhtscodecs2:arm64. 234s Preparing to unpack .../07-libhtscodecs2_1.6.1-1_arm64.deb ... 234s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 234s Selecting previously unselected package libhts3t64:arm64. 234s Preparing to unpack .../08-libhts3t64_1.20+ds-2_arm64.deb ... 234s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 234s Selecting previously unselected package liblapack3:arm64. 234s Preparing to unpack .../09-liblapack3_3.12.0-4_arm64.deb ... 234s Unpacking liblapack3:arm64 (3.12.0-4) ... 235s Selecting previously unselected package liblbfgsb0:arm64. 235s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 235s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 235s Selecting previously unselected package liblzf1:arm64. 235s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 235s Unpacking liblzf1:arm64 (3.6-4) ... 235s Selecting previously unselected package python3-numpy. 235s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-12_arm64.deb ... 235s Unpacking python3-numpy (1:1.26.4+ds-12) ... 235s Selecting previously unselected package python3-h5py-serial. 235s Preparing to unpack .../13-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 235s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 235s Selecting previously unselected package python3-dateutil. 235s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 235s Unpacking python3-dateutil (2.9.0-3) ... 235s Selecting previously unselected package python3-tz. 235s Preparing to unpack .../15-python3-tz_2024.2-1_all.deb ... 235s Unpacking python3-tz (2024.2-1) ... 235s Selecting previously unselected package python3-pandas-lib:arm64. 235s Preparing to unpack .../16-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ... 235s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 236s Selecting previously unselected package python3-pandas. 236s Preparing to unpack .../17-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 236s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 236s Selecting previously unselected package python3-decorator. 236s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 236s Unpacking python3-decorator (5.1.1-5) ... 236s Selecting previously unselected package python3-fastjsonschema. 236s Preparing to unpack .../19-python3-fastjsonschema_2.21.1-1_all.deb ... 236s Unpacking python3-fastjsonschema (2.21.1-1) ... 236s Selecting previously unselected package python3-platformdirs. 236s Preparing to unpack .../20-python3-platformdirs_4.3.6-1_all.deb ... 236s Unpacking python3-platformdirs (4.3.6-1) ... 236s Selecting previously unselected package python3-traitlets. 236s Preparing to unpack .../21-python3-traitlets_5.14.3+really5.14.3-1_all.deb ... 236s Unpacking python3-traitlets (5.14.3+really5.14.3-1) ... 236s Selecting previously unselected package python3-jupyter-core. 236s Preparing to unpack .../22-python3-jupyter-core_5.7.2-5_all.deb ... 236s Unpacking python3-jupyter-core (5.7.2-5) ... 236s Selecting previously unselected package python3-nbformat. 236s Preparing to unpack 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(4.67.1-1) ... 240s Selecting previously unselected package python3-h5py. 240s Preparing to unpack .../29-python3-h5py_3.11.0-8ubuntu3_all.deb ... 240s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 240s Selecting previously unselected package pycoqc. 240s Preparing to unpack .../30-pycoqc_2.5.2+dfsg-3_all.deb ... 240s Unpacking pycoqc (2.5.2+dfsg-3) ... 240s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 240s Setting up python3-tenacity (8.5.0-0ubuntu1) ... 240s Setting up python3-tqdm (4.67.1-1) ... 241s Setting up libdeflate0:arm64 (1.22-1) ... 241s Setting up libaec0:arm64 (1.1.3-1) ... 241s Setting up python3-platformdirs (4.3.6-1) ... 241s Setting up python3-tz (2024.2-1) ... 241s Setting up python3-decorator (5.1.1-5) ... 241s Setting up libblas3:arm64 (3.12.0-4) ... 241s 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 241s Setting up liblzf1:arm64 (3.6-4) ... 241s Setting up libgfortran5:arm64 (14.2.0-12ubuntu1) ... 241s Setting up python3-fastjsonschema (2.21.1-1) ... 242s Setting up python3-traitlets (5.14.3+really5.14.3-1) ... 242s Setting up libhts3t64:arm64 (1.20+ds-2) ... 242s Setting up python3-dateutil (2.9.0-3) ... 242s Setting up python3-jupyter-core (5.7.2-5) ... 242s Setting up libsz2:arm64 (1.1.3-1) ... 242s Setting up liblapack3:arm64 (3.12.0-4) ... 242s 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 242s Setting up python3-pysam (0.22.1+ds-2build1) ... 243s Setting up python3-nbformat (5.9.1-1) ... 243s Setting up python3-plotly (5.20.0+dfsg-1) ... 253s Setting up python3-numpy (1:1.26.4+ds-12) ... 256s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-5ubuntu1) ... 256s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 256s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-5ubuntu1) ... 256s Setting up python3-scipy (1.14.1-3ubuntu1) ... 260s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 260s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 260s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 267s Setting up python3-h5py (3.11.0-8ubuntu3) ... 267s Setting up pycoqc (2.5.2+dfsg-3) ... 267s Processing triggers for libc-bin (2.40-4ubuntu1) ... 267s Processing triggers for man-db (2.13.0-1) ... 269s autopkgtest [14:06:59]: test run-unit-test: [----------------------- 269s Test 1 271s Checking arguments values 271s Check input data files 271s Parse data files 271s Merge data 271s Cleaning data 271s Loading plotting interface 272s PASS 272s 272s Test 2 273s Checking arguments values 273s Check input data files 273s Parse data files 273s Merge data 273s Cleaning data 273s Loading plotting interface 274s PASS 274s 274s Test 3 275s Checking arguments values 275s Check input data files 275s Parse data files 275s Merge data 275s Cleaning data 275s Loading plotting interface 276s PASS 276s 276s Test 4 277s Checking arguments values 277s Check input data files 277s Parse data files 277s Merge data 277s Cleaning data 277s Loading plotting interface 278s PASS 278s 278s Test 5 279s Checking arguments values 279s Check input data files 279s Parse data files 279s Merge data 279s Cleaning data 279s Loading plotting interface 280s PASS 280s 280s Test 6 281s PASS 281s 281s Test 7 282s Checking arguments values 282s Check input data files 282s Parse data files 282s Merge data 282s Cleaning data 283s Loading plotting interface 284s PASS 284s 284s Test 8 285s 0 reads [00:00, ? reads/s] 22 reads [00:00, 431.16 reads/s] 285s Total reads: 22 / Average speed: 302.76 reads/s 285s 285s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template 285s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out 285s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out 285s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out 285s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out 285s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out 285s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out 285s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out 285s 6af04302-04c8-4d8d-8e87-aa69178b3f24 40ebe55356ada6c830fa793745ef4c498d896c73 36 26 832 8.234 filtered_out 285s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out 285s PASS 285s 285s Test 9 286s Check input data and options 286s Start processing fast5 files 286s 0 reads [00:00, ? reads/s] 22 reads [00:00, 620.47 reads/s] 286s Overall counts valid files: 22 286s 286s fields found mean_qscore_template: 22 286s called_events: 22 286s duration: 22 286s strand_score: 22 286s 286s fields not found 286s Total reads: 22 / Average speed: 382.09 reads/s 286s 286s mean_qscore_template called_events duration strand_score 286s 8.23 2778 51387 -0.0007 286s 7.337 1972 29589 -0.0009 286s 8.124 2978 44675 -0.0005 286s 9.407 2848 42730 -0.0003 286s 8.119 3181 47720 -0.0004 286s 7.742 2142 32138 -0.0004 286s 8.304 1547 23218 -0.0008 286s 7.414 3017 45267 -0.0002 286s 8.234 1827 27409 -0.0011 286s PASS 286s 286s Test 10 287s Check input data and options 287s Start processing fast5 files 287s 0 reads [00:00, ? reads/s] 22 reads [00:00, 610.50 reads/s] 287s Overall counts valid files: 22 287s 287s fields found read_id: 22 287s run_id: 22 287s channel: 22 287s start_time: 22 287s sequence_length_template: 22 287s mean_qscore_template: 22 287s calibration_strand_genome_template: 22 287s 287s fields not found barcode_arrangement: 22 287s 287s Total reads: 22 / Average speed: 380.42 reads/s 287s 288s read_id run_id channel start_time sequence_length_template mean_qscore_template calibration_strand_genome_template path 288s 151757ea-53de-44b1-b86e-f823511af02a 40ebe55356ada6c830fa793745ef4c498d896c73 191 13 568 8.23 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_191_strand.fast5 288s 3e81c32a-f2ee-4719-a88d-e0affe93d26f 40ebe55356ada6c830fa793745ef4c498d896c73 348 24 1137 8.124 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_348_strand.fast5 288s bcb20156-a5fe-4daa-aad9-b62c286e468d 40ebe55356ada6c830fa793745ef4c498d896c73 192 21 306 7.337 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_192_strand.fast5 288s 0ef36fa0-7c3f-47f5-8410-027f50724701 40ebe55356ada6c830fa793745ef4c498d896c73 108 26 915 9.407 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_108_strand.fast5 288s 3f09025f-3d2c-4f84-9ea6-63dba736b649 40ebe55356ada6c830fa793745ef4c498d896c73 418 17 593 7.742 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_418_strand.fast5 288s 9a1c5296-2ab1-4abd-8d50-e059754cf332 40ebe55356ada6c830fa793745ef4c498d896c73 319 33 1235 8.119 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_319_strand.fast5 288s 1f83ee80-ac29-46be-b8bc-9dc9325f1fa7 40ebe55356ada6c830fa793745ef4c498d896c73 382 35 819 7.414 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_382_strand.fast5 288s e6a8e4d0-7b3c-471a-be26-fa7857d12663 40ebe55356ada6c830fa793745ef4c498d896c73 318 15 392 8.304 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_318_strand.fast5 288s 97205d42-93ac-4c99-af78-e553f7d1ff83 40ebe55356ada6c830fa793745ef4c498d896c73 343 26 1584 8.987 filtered_out /tmp/autopkgtest.55wif3/autopkgtest_tmp/datafast5/20180625_FAH77625_MN23126_sequencing_run_S1_57529_read_10_ch_343_strand.fast5 288s PASS 288s 288s Test 11 288s Import data from sequencing summary file(s) and cleanup 288s Read files and import in a dataframe 288s Check input data files 288s Parse data files 289s Merge data 289s Cleanup missing barcodes values 289s Cleaning up low frequency barcodes 289s Split data per barcode 289s Processing data for Barcode barcode02 289s Processing data for Barcode barcode07 289s Processing data for Barcode barcode08 289s Processing data for Barcode barcode09 289s Processing data for Barcode barcode10 289s Processing data for Barcode barcode11 290s Processing data for Barcode barcode12 290s Processing data for Barcode unclassified 290s Barcode Counts 290s Counts Write 290s barcode02 2 False 290s barcode07 1 False 290s barcode08 30 False 290s barcode09 9945 True 290s barcode10 12644 True 290s barcode11 13594 True 290s barcode12 9813 True 290s unclassified 3971 False 290s PASS 290s 290s Test 12 291s General info 291s package_name: pycoQC 291s package_version: 2.5.2 291s timestamp: 2025-01-03 14:07:21.256199 291s 291s Runtime options 291s summary_file: ['Guppy-basecall-1D-DNA_sequencing_summary.txt'] 291s barcode_file: ['Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt'] 291s output_dir: results/ 291s output_unclassified: False 291s min_barcode_percent: 0.1 291s verbose: True 291s quiet: False 291s 291s Import data from sequencing summary file(s) and cleanup 291s Read files and import in a dataframe 291s Check input data files 291s Sequencing summary files found: Guppy-basecall-1D-DNA_sequencing_summary.txt 291s Barcode files found: Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt 291s Parse data files 291s Parse summary files 291s 3,999 reads found in initial file 291s Parse barcode files 291s Found valid Deepbinner barcode file 291s 3,775 reads with barcodes assigned 291s Merge data 291s Cleanup missing barcodes values 291s Cleaning up low frequency barcodes 291s Split data per barcode 291s Processing data for Barcode 1 291s Processing data for Barcode 2 291s Processing data for Barcode 3 291s Processing data for Barcode 4 291s Processing data for Barcode 5 291s Processing data for Barcode 6 291s Processing data for Barcode 7 291s Processing data for Barcode 8 291s Processing data for Barcode unclassified 291s Barcode Counts 291s Counts Write 291s 1 534 True 291s 2 206 True 291s 3 562 True 291s 4 579 True 291s 5 590 True 291s 6 655 True 291s 7 271 True 291s 8 378 True 291s unclassified 224 False 291s PASS 291s 291s Check if files really exist 291s PASS 291s 291s autopkgtest [14:07:21]: test run-unit-test: -----------------------] 292s autopkgtest [14:07:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 292s run-unit-test PASS 292s autopkgtest [14:07:22]: @@@@@@@@@@@@@@@@@@@@ summary 292s run-unit-test PASS 310s nova [W] Using flock in prodstack6-arm64 310s Creating nova instance adt-plucky-arm64-pycoqc-20250103-140230-juju-7f2275-prod-proposed-migration-environment-2-fae6503b-bb0e-447d-aa77-96c8b7411356 from image adt/ubuntu-plucky-arm64-server-20250102.img (UUID 4cb073f4-4206-4362-b576-2406cb25ddd8)... 310s nova [W] Timed out waiting for e4d4904c-6a00-48f9-b014-da8e7304b6ef to get deleted.