0s autopkgtest [11:31:01]: starting date and time: 2024-11-13 11:31:01+0000
  0s autopkgtest [11:31:01]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [11:31:01]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c26mowyn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade circlator --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-8.secgroup --name adt-plucky-ppc64el-circlator-20241113-110058-juju-7f2275-prod-proposed-migration-environment-20-6e979c26-b293-4f58-affd-6384b0786285 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 81s autopkgtest [11:32:22]: testbed dpkg architecture: ppc64el
 82s autopkgtest [11:32:23]: testbed apt version: 2.9.8
 82s autopkgtest [11:32:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 83s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 83s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 83s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [86.2 kB]
 83s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [588 kB]
 83s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [19.6 kB]
 84s Fetched 1715 kB in 1s (1674 kB/s)
 84s Reading package lists...
 86s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s Calculating upgrade...
 87s The following NEW packages will be installed:
 87s   python3.13-gdbm
 87s The following packages will be upgraded:
 87s   libpython3-stdlib python3 python3-gdbm python3-minimal
 87s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 87s Need to get 102 kB of archives.
 87s After this operation, 141 kB of additional disk space will be used.
 87s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
 88s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
 88s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
 88s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
 88s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
 88s Fetched 102 kB in 0s (290 kB/s)
 88s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
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(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 ... 73767 files and directories currently installed.)
 88s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
 88s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 88s Setting up python3-minimal (3.12.7-1) ...
 89s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(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 ... 73767 files and directories currently installed.)
 89s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ...
 89s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 89s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ...
 89s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ...
 89s Selecting previously unselected package python3.13-gdbm.
 89s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ...
 89s Unpacking python3.13-gdbm (3.13.0-2) ...
 89s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ...
 89s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
 89s Setting up python3.13-gdbm (3.13.0-2) ...
 89s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
 89s Setting up python3 (3.12.7-1) ...
 89s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
 89s Processing triggers for man-db (2.12.1-3) ...
 90s Reading package lists...
 91s Building dependency tree...
 91s Reading state information...
 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 91s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 91s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 91s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 92s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 93s Reading package lists...
 93s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 93s Calculating upgrade...
 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 93s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 97s autopkgtest [11:32:38]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
 97s autopkgtest [11:32:38]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
 99s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (dsc) [1672 B]
 99s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (tar) [5724 kB]
 99s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (diff) [6152 B]
 99s gpgv: Signature made Sat Dec  2 21:39:17 2023 UTC
 99s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
 99s gpgv: Can't check signature: No public key
 99s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found
100s autopkgtest [11:32:41]: testing package circlator version 1.5.6-11
100s autopkgtest [11:32:41]: build not needed
101s autopkgtest [11:32:42]: test run-unit-test: preparing testbed
104s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s Starting pkgProblemResolver with broken count: 0
104s Starting 2 pkgProblemResolver with broken count: 0
104s Done
105s The following additional packages will be installed:
105s   aglfn binfmt-support bwa ca-certificates-java canu circlator
105s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
105s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
105s   jarwrapper java-common libaom3 libapache-pom-java
105s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
105s   libcommons-compress-java libcommons-io-java libcommons-parent-java
105s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
105s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
105s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
105s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
105s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
105s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
105s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0
105s   libsnappy1v5 libssw-java libthai-data libthai0 libtiff6 libwebp7 libwebpmux3
105s   libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap mummer
105s   openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
105s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
105s   python3-pluggy python3-pymummer python3-pysam python3-pytest python3.13
105s   python3.13-minimal samtools
105s Suggested packages:
105s   nanopolish default-jre gnuplot-doc libatinject-jsr330-api-java-doc
105s   libasm-java libxz-java libgd-tools libheif-plugin-x265
105s   libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
105s   libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar
105s   libheif-plugin-rav1e libheif-plugin-svtenc libjsr305-java-doc liblcms2-utils
105s   pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
105s   fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic
105s   python-lxml-doc python-openpyxl-doc python3.13-venv python3.13-doc cwltool
105s Recommended packages:
105s   spades fonts-liberation groff libheif-plugin-aomenc libcups2t64
105s   libasound2t64 python3-bs4 python3-cssselect python3-html5lib python3-pil
105s The following NEW packages will be installed:
105s   aglfn autopkgtest-satdep binfmt-support bwa ca-certificates-java canu
105s   circlator default-jre-headless fastaq fastjar fontconfig fontconfig-config
105s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
105s   jarwrapper java-common libaom3 libapache-pom-java
105s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
105s   libcommons-compress-java libcommons-io-java libcommons-parent-java
105s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
105s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
105s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
105s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
105s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
105s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
105s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0
105s   libsnappy1v5 libssw-java libthai-data libthai0 libtiff6 libwebp7 libwebpmux3
105s   libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap mummer
105s   openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
105s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
105s   python3-pluggy python3-pymummer python3-pysam python3-pytest python3.13
105s   python3.13-minimal samtools
105s 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded.
105s Need to get 104 MB/104 MB of archives.
105s After this operation, 392 MB of additional disk space will be used.
105s Get:1 /tmp/autopkgtest.WuCRGJ/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
105s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el binfmt-support ppc64el 2.2.2-7 [66.8 kB]
105s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB]
105s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB]
106s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bwa ppc64el 0.7.18-1 [231 kB]
106s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el ca-certificates-java all 20240118 [11.6 kB]
106s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB]
106s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsnappy1v5 ppc64el 1.2.1-1 [33.4 kB]
106s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfilesys-df-perl ppc64el 0.92-7build5 [11.2 kB]
106s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el java-common all 0.76 [6852 B]
106s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB]
106s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB]
106s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
106s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcsclite1 ppc64el 2.3.0-1 [30.8 kB]
106s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el openjdk-21-jre-headless ppc64el 21.0.5+11-1 [45.7 MB]
107s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el default-jre-headless ppc64el 2:1.21-76 [3184 B]
107s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastjar ppc64el 2:0.98-7 [79.7 kB]
107s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el jarwrapper all 0.80 [9800 B]
107s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libapache-pom-java all 33-2 [5874 B]
107s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-parent-java all 56-1 [10.7 kB]
107s Get:21 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-codec-java all 1.17.1-1 [302 kB]
107s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-io-java all 2.17.0-1 [457 kB]
107s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcommons-compress-java all 1.27.1-2 [610 kB]
107s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
108s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
108s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liberror-prone-java all 2.18.0-1 [22.5 kB]
108s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjsr305-java all 0.1~+svn49-11 [27.0 kB]
108s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libguava-java all 32.0.1-1 [2692 kB]
108s Get:29 http://ftpmaster.internal/ubuntu plucky/universe ppc64el jaligner all 1.0+dfsg-11 [136 kB]
108s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libssw-java ppc64el 1.1-15 [20.4 kB]
108s Get:31 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mhap all 2.1.3+dfsg-3 [160 kB]
108s Get:32 http://ftpmaster.internal/ubuntu plucky/universe ppc64el aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
108s Get:33 http://ftpmaster.internal/ubuntu plucky/universe ppc64el gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
108s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
108s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
108s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
108s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
108s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
108s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
108s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
108s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
108s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
108s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB]
108s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libaom3 ppc64el 3.11.0~rc1-1 [3022 kB]
108s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-aomdec ppc64el 1.18.1-2 [11.2 kB]
108s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libde265-0 ppc64el 1.0.15-1build4 [284 kB]
108s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif-plugin-libde265 ppc64el 1.18.1-2 [9068 B]
108s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libheif1 ppc64el 1.18.1-2 [340 kB]
108s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB]
108s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
108s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB]
108s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB]
108s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB]
108s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
108s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB]
108s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB]
108s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
108s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxpm4 ppc64el 1:3.5.17-1build2 [49.9 kB]
108s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgd3 ppc64el 2.3.3-12ubuntu3 [165 kB]
108s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblua5.4-0 ppc64el 5.4.6-3build2 [216 kB]
108s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB]
108s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB]
108s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB]
108s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB]
108s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.54.0+ds-3 [272 kB]
108s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.54.0+ds-3 [57.5 kB]
108s Get:67 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.54.0+ds-3 [30.6 kB]
108s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB]
108s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el gnuplot-nox ppc64el 6.0.0+dfsg1-1ubuntu3 [1225 kB]
108s Get:70 http://ftpmaster.internal/ubuntu plucky/universe ppc64el canu ppc64el 2.2+dfsg-5 [1763 kB]
108s Get:71 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB]
108s Get:72 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB]
108s Get:73 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.20-3 [676 kB]
108s Get:74 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastaq all 3.17.0-8 [48.2 kB]
108s Get:75 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-et-xmlfile all 2.0.0-1 [79.4 kB]
108s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB]
108s Get:77 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB]
108s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
108s Get:79 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB]
108s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB]
108s Get:81 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pymummer all 0.11.0-4 [17.1 kB]
108s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB]
109s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el prodigal ppc64el 1:2.6.3-6 [1314 kB]
109s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el circlator all 1.5.6-11 [4618 kB]
109s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB]
109s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB]
109s Get:87 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B]
109s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B]
109s Get:89 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB]
109s Get:90 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB]
109s Fetched 104 MB in 4s (25.8 MB/s)
109s Selecting previously unselected package binfmt-support.
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109s Preparing to unpack .../00-binfmt-support_2.2.2-7_ppc64el.deb ...
109s Unpacking binfmt-support (2.2.2-7) ...
109s Selecting previously unselected package libpython3.13-minimal:ppc64el.
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110s Selecting previously unselected package python3.13-minimal.
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110s Selecting previously unselected package bwa.
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110s Unpacking bwa (0.7.18-1) ...
110s Selecting previously unselected package ca-certificates-java.
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110s Selecting previously unselected package libgomp1:ppc64el.
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110s Selecting previously unselected package libfilesys-df-perl.
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110s Selecting previously unselected package java-common.
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110s Selecting previously unselected package liblcms2-2:ppc64el.
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110s Selecting previously unselected package libjpeg-turbo8:ppc64el.
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110s Selecting previously unselected package libjpeg8:ppc64el.
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110s Selecting previously unselected package libpcsclite1:ppc64el.
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110s Selecting previously unselected package openjdk-21-jre-headless:ppc64el.
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111s Selecting previously unselected package default-jre-headless.
111s Preparing to unpack .../14-default-jre-headless_2%3a1.21-76_ppc64el.deb ...
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111s Selecting previously unselected package fastjar.
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112s Selecting previously unselected package libapache-pom-java.
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112s Selecting previously unselected package libcommons-parent-java.
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112s Selecting previously unselected package libcommons-codec-java.
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112s Selecting previously unselected package libcommons-io-java.
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112s Selecting previously unselected package libcommons-compress-java.
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112s Selecting previously unselected package libfastutil-java.
112s Preparing to unpack .../22-libfastutil-java_8.5.15+dfsg-1_all.deb ...
112s Unpacking libfastutil-java (8.5.15+dfsg-1) ...
112s Selecting previously unselected package libatinject-jsr330-api-java.
112s Preparing to unpack .../23-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
112s Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ...
112s Selecting previously unselected package liberror-prone-java.
112s Preparing to unpack .../24-liberror-prone-java_2.18.0-1_all.deb ...
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112s Selecting previously unselected package libjsr305-java.
112s Preparing to unpack .../25-libjsr305-java_0.1~+svn49-11_all.deb ...
112s Unpacking libjsr305-java (0.1~+svn49-11) ...
112s Selecting previously unselected package libguava-java.
112s Preparing to unpack .../26-libguava-java_32.0.1-1_all.deb ...
112s Unpacking libguava-java (32.0.1-1) ...
112s Selecting previously unselected package jaligner.
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112s Unpacking jaligner (1.0+dfsg-11) ...
112s Selecting previously unselected package libssw-java.
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112s Unpacking libssw-java (1.1-15) ...
112s Selecting previously unselected package mhap.
112s Preparing to unpack .../29-mhap_2.1.3+dfsg-3_all.deb ...
112s Unpacking mhap (2.1.3+dfsg-3) ...
112s Selecting previously unselected package aglfn.
112s Preparing to unpack .../30-aglfn_1.7+git20191031.4036a9c-2_all.deb ...
112s Unpacking aglfn (1.7+git20191031.4036a9c-2) ...
112s Selecting previously unselected package gnuplot-data.
112s Preparing to unpack .../31-gnuplot-data_6.0.0+dfsg1-1ubuntu3_all.deb ...
112s Unpacking gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
112s Selecting previously unselected package fonts-dejavu-mono.
112s Preparing to unpack .../32-fonts-dejavu-mono_2.37-8_all.deb ...
112s Unpacking fonts-dejavu-mono (2.37-8) ...
112s Selecting previously unselected package fonts-dejavu-core.
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112s Unpacking fonts-dejavu-core (2.37-8) ...
112s Selecting previously unselected package fontconfig-config.
112s Preparing to unpack .../34-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ...
113s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
113s Selecting previously unselected package libfontconfig1:ppc64el.
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113s Selecting previously unselected package libpixman-1-0:ppc64el.
113s Preparing to unpack .../36-libpixman-1-0_0.44.0-3_ppc64el.deb ...
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113s Selecting previously unselected package libxcb-render0:ppc64el.
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113s Selecting previously unselected package libxcb-shm0:ppc64el.
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113s Selecting previously unselected package libxrender1:ppc64el.
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113s Selecting previously unselected package libcairo2:ppc64el.
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113s Selecting previously unselected package libsharpyuv0:ppc64el.
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113s Selecting previously unselected package libaom3:ppc64el.
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113s Unpacking libaom3:ppc64el (3.11.0~rc1-1) ...
113s Selecting previously unselected package libheif-plugin-aomdec:ppc64el.
113s Preparing to unpack .../43-libheif-plugin-aomdec_1.18.1-2_ppc64el.deb ...
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113s Selecting previously unselected package libde265-0:ppc64el.
113s Preparing to unpack .../44-libde265-0_1.0.15-1build4_ppc64el.deb ...
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113s Selecting previously unselected package libheif-plugin-libde265:ppc64el.
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113s Unpacking libheif-plugin-libde265:ppc64el (1.18.1-2) ...
113s Selecting previously unselected package libheif1:ppc64el.
113s Preparing to unpack .../46-libheif1_1.18.1-2_ppc64el.deb ...
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113s Selecting previously unselected package libimagequant0:ppc64el.
113s Preparing to unpack .../47-libimagequant0_2.18.0-1build1_ppc64el.deb ...
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113s Selecting previously unselected package libgraphite2-3:ppc64el.
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113s Selecting previously unselected package libharfbuzz0b:ppc64el.
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113s Selecting previously unselected package libraqm0:ppc64el.
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113s Selecting previously unselected package libdeflate0:ppc64el.
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113s Selecting previously unselected package libjbig0:ppc64el.
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113s Selecting previously unselected package liblerc4:ppc64el.
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113s Selecting previously unselected package libwebp7:ppc64el.
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113s Selecting previously unselected package libtiff6:ppc64el.
113s Preparing to unpack .../55-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ...
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113s Selecting previously unselected package libxpm4:ppc64el.
113s Preparing to unpack .../56-libxpm4_1%3a3.5.17-1build2_ppc64el.deb ...
113s Unpacking libxpm4:ppc64el (1:3.5.17-1build2) ...
113s Selecting previously unselected package libgd3:ppc64el.
113s Preparing to unpack .../57-libgd3_2.3.3-12ubuntu3_ppc64el.deb ...
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113s Selecting previously unselected package liblua5.4-0:ppc64el.
113s Preparing to unpack .../58-liblua5.4-0_5.4.6-3build2_ppc64el.deb ...
113s Unpacking liblua5.4-0:ppc64el (5.4.6-3build2) ...
113s Selecting previously unselected package fontconfig.
113s Preparing to unpack .../59-fontconfig_2.15.0-1.1ubuntu2_ppc64el.deb ...
113s Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
113s Selecting previously unselected package libthai-data.
113s Preparing to unpack .../60-libthai-data_0.1.29-2build1_all.deb ...
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113s Selecting previously unselected package libdatrie1:ppc64el.
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113s Selecting previously unselected package libthai0:ppc64el.
113s Preparing to unpack .../62-libthai0_0.1.29-2build1_ppc64el.deb ...
113s Unpacking libthai0:ppc64el (0.1.29-2build1) ...
113s Selecting previously unselected package libpango-1.0-0:ppc64el.
113s Preparing to unpack .../63-libpango-1.0-0_1.54.0+ds-3_ppc64el.deb ...
113s Unpacking libpango-1.0-0:ppc64el (1.54.0+ds-3) ...
114s Selecting previously unselected package libpangoft2-1.0-0:ppc64el.
114s Preparing to unpack .../64-libpangoft2-1.0-0_1.54.0+ds-3_ppc64el.deb ...
114s Unpacking libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ...
114s Selecting previously unselected package libpangocairo-1.0-0:ppc64el.
114s Preparing to unpack .../65-libpangocairo-1.0-0_1.54.0+ds-3_ppc64el.deb ...
114s Unpacking libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ...
114s Selecting previously unselected package libwebpmux3:ppc64el.
114s Preparing to unpack .../66-libwebpmux3_1.4.0-0.1_ppc64el.deb ...
114s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ...
114s Selecting previously unselected package gnuplot-nox.
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114s Unpacking gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
114s Selecting previously unselected package canu.
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114s Unpacking canu (2.2+dfsg-5) ...
114s Selecting previously unselected package libhtscodecs2:ppc64el.
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114s Selecting previously unselected package libhts3t64:ppc64el.
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114s Selecting previously unselected package samtools.
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114s Unpacking samtools (1.20-3) ...
114s Selecting previously unselected package fastaq.
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114s Unpacking fastaq (3.17.0-8) ...
114s Selecting previously unselected package python3-et-xmlfile.
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114s Selecting previously unselected package libxslt1.1:ppc64el.
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114s Selecting previously unselected package python3-packaging.
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114s Unpacking python3-packaging (24.1-1) ...
114s Selecting previously unselected package mummer.
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114s Selecting previously unselected package python3-pymummer.
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114s Selecting previously unselected package python3-pysam.
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114s Selecting previously unselected package prodigal.
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114s Selecting previously unselected package circlator.
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115s Selecting previously unselected package python3-iniconfig.
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115s Unpacking python3-iniconfig (1.1.1-2) ...
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115s Unpacking python3-pluggy (1.5.0-1) ...
115s Selecting previously unselected package python3-pytest.
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115s Unpacking python3-pytest (8.3.3-1) ...
115s Selecting previously unselected package autopkgtest-satdep.
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115s Unpacking autopkgtest-satdep (0) ...
115s Setting up libhtscodecs2:ppc64el (1.6.1-1) ...
115s Setting up fastjar (2:0.98-7) ...
115s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
115s Setting up liblcms2-2:ppc64el (2.16-2) ...
115s Setting up python3-iniconfig (1.1.1-2) ...
115s Setting up libpixman-1-0:ppc64el (0.44.0-3) ...
115s Setting up libfastutil-java (8.5.15+dfsg-1) ...
115s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ...
115s Setting up libaom3:ppc64el (3.11.0~rc1-1) ...
115s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ...
115s Setting up libjsr305-java (0.1~+svn49-11) ...
115s Setting up libxpm4:ppc64el (1:3.5.17-1build2) ...
115s Setting up java-common (0.76) ...
115s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ...
115s Setting up libdatrie1:ppc64el (0.2.13-3build1) ...
115s Setting up libxcb-render0:ppc64el (1.17.0-2) ...
115s Setting up prodigal (1:2.6.3-6) ...
115s Setting up bwa (0.7.18-1) ...
115s Setting up libfilesys-df-perl (0.92-7build5) ...
115s Setting up libdeflate0:ppc64el (1.22-1) ...
115s Setting up libxcb-shm0:ppc64el (1.17.0-2) ...
115s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ...
115s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ...
115s Setting up libssw-java (1.1-15) ...
115s Setting up libsnappy1v5:ppc64el (1.2.1-1) ...
115s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ...
115s Setting up python3-packaging (24.1-1) ...
116s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
116s Setting up libapache-pom-java (33-2) ...
116s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
116s Setting up libimagequant0:ppc64el (2.18.0-1build1) ...
116s Setting up fonts-dejavu-mono (2.37-8) ...
116s Setting up binfmt-support (2.2.2-7) ...
116s update-binfmts: warning: python3.12 already enabled in kernel.
116s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

117s Setting up fonts-dejavu-core (2.37-8) ...
117s Setting up libpcsclite1:ppc64el (2.3.0-1) ...
117s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ...
117s Setting up python3-pluggy (1.5.0-1) ...
117s Setting up libwebp7:ppc64el (1.4.0-0.1) ...
117s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ...
117s Setting up mummer (3.23+dfsg-8) ...
117s Setting up python3-et-xmlfile (2.0.0-1) ...
117s Setting up libhts3t64:ppc64el (1.20+ds-1) ...
117s Setting up liblua5.4-0:ppc64el (5.4.6-3build2) ...
117s Setting up python3.13-minimal (3.13.0-2) ...
118s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ...
118s Setting up libthai-data (0.1.29-2build1) ...
118s Setting up ca-certificates-java (20240118) ...
118s No JRE found. Skipping Java certificates setup.
118s Setting up libde265-0:ppc64el (1.0.15-1build4) ...
118s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ...
118s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ...
118s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
118s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
118s Setting up python3-pysam (0.22.1+ds-2) ...
119s Setting up openjdk-21-jre-headless:ppc64el (21.0.5+11-1) ...
119s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/java to provide /usr/bin/java (java) in auto mode
119s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
119s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
119s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
119s update-alternatives: using /usr/lib/jvm/java-21-openjdk-ppc64el/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
119s Setting up jarwrapper (0.80) ...
119s Setting up python3.13 (3.13.0-2) ...
120s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
120s Setting up python3-pytest (8.3.3-1) ...
121s Setting up libcommons-parent-java (56-1) ...
121s Setting up python3-all (3.12.7-1) ...
121s Setting up samtools (1.20-3) ...
121s Setting up libthai0:ppc64el (0.1.29-2build1) ...
121s Setting up libraqm0:ppc64el (0.10.1-1build1) ...
121s Setting up python3-lxml:ppc64el (5.3.0-1) ...
121s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
121s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
121s Setting up libcommons-codec-java (1.17.1-1) ...
121s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
123s Regenerating fonts cache... done.
123s Setting up libcommons-io-java (2.17.0-1) ...
123s Setting up fastaq (3.17.0-8) ...
123s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
123s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
123s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
123s   gbk_regex = re.compile('^LOCUS\s+\S')
123s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
123s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
123s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
123s   gbk_regex = re.compile('^LOCUS\s+\S')
123s Setting up libpango-1.0-0:ppc64el (1.54.0+ds-3) ...
123s Setting up libcairo2:ppc64el (1.18.2-2) ...
123s Setting up python3-pymummer (0.11.0-4) ...
124s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
124s Setting up libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ...
124s Setting up libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ...
124s Setting up libcommons-compress-java (1.27.1-2) ...
124s Setting up libheif-plugin-aomdec:ppc64el (1.18.1-2) ...
124s Setting up libheif-plugin-libde265:ppc64el (1.18.1-2) ...
124s Setting up liberror-prone-java (2.18.0-1) ...
124s Setting up libheif1:ppc64el (1.18.1-2) ...
124s Setting up libguava-java (32.0.1-1) ...
124s Setting up libgd3:ppc64el (2.3.3-12ubuntu3) ...
124s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
124s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
124s Processing triggers for install-info (7.1.1-1) ...
125s Processing triggers for libc-bin (2.40-1ubuntu3) ...
125s Processing triggers for systemd (256.5-2ubuntu4) ...
125s Processing triggers for man-db (2.12.1-3) ...
126s Processing triggers for ca-certificates-java (20240118) ...
127s Adding debian:ACCVRAIZ1.pem
127s Adding debian:AC_RAIZ_FNMT-RCM.pem
127s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
127s Adding debian:ANF_Secure_Server_Root_CA.pem
127s Adding debian:Actalis_Authentication_Root_CA.pem
127s Adding debian:AffirmTrust_Commercial.pem
127s Adding debian:AffirmTrust_Networking.pem
127s Adding debian:AffirmTrust_Premium.pem
127s Adding debian:AffirmTrust_Premium_ECC.pem
127s Adding debian:Amazon_Root_CA_1.pem
127s Adding debian:Amazon_Root_CA_2.pem
127s Adding debian:Amazon_Root_CA_3.pem
127s Adding debian:Amazon_Root_CA_4.pem
127s Adding debian:Atos_TrustedRoot_2011.pem
127s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
127s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
127s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
127s Adding debian:BJCA_Global_Root_CA1.pem
127s Adding debian:BJCA_Global_Root_CA2.pem
127s Adding debian:Baltimore_CyberTrust_Root.pem
127s Adding debian:Buypass_Class_2_Root_CA.pem
127s Adding debian:Buypass_Class_3_Root_CA.pem
127s Adding debian:CA_Disig_Root_R2.pem
127s Adding debian:CFCA_EV_ROOT.pem
127s Adding debian:COMODO_Certification_Authority.pem
127s Adding debian:COMODO_ECC_Certification_Authority.pem
127s Adding debian:COMODO_RSA_Certification_Authority.pem
127s Adding debian:Certainly_Root_E1.pem
127s Adding debian:Certainly_Root_R1.pem
127s Adding debian:Certigna.pem
127s Adding debian:Certigna_Root_CA.pem
127s Adding debian:Certum_EC-384_CA.pem
127s Adding debian:Certum_Trusted_Network_CA.pem
127s Adding debian:Certum_Trusted_Network_CA_2.pem
127s Adding debian:Certum_Trusted_Root_CA.pem
127s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
127s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
127s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
127s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
127s Adding debian:Comodo_AAA_Services_root.pem
127s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
127s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
127s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
127s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
127s Adding debian:DigiCert_Assured_ID_Root_CA.pem
127s Adding debian:DigiCert_Assured_ID_Root_G2.pem
127s Adding debian:DigiCert_Assured_ID_Root_G3.pem
127s Adding debian:DigiCert_Global_Root_CA.pem
127s Adding debian:DigiCert_Global_Root_G2.pem
127s Adding debian:DigiCert_Global_Root_G3.pem
127s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
127s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
127s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
127s Adding debian:DigiCert_Trusted_Root_G4.pem
127s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
127s Adding debian:Entrust_Root_Certification_Authority.pem
127s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
127s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
127s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
127s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
127s Adding debian:GLOBALTRUST_2020.pem
127s Adding debian:GTS_Root_R1.pem
127s Adding debian:GTS_Root_R2.pem
127s Adding debian:GTS_Root_R3.pem
127s Adding debian:GTS_Root_R4.pem
127s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
127s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
127s Adding debian:GlobalSign_Root_CA.pem
127s Adding debian:GlobalSign_Root_CA_-_R3.pem
127s Adding debian:GlobalSign_Root_CA_-_R6.pem
127s Adding debian:GlobalSign_Root_E46.pem
127s Adding debian:GlobalSign_Root_R46.pem
127s Adding debian:Go_Daddy_Class_2_CA.pem
127s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
127s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
127s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
127s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
127s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
127s Adding debian:HiPKI_Root_CA_-_G1.pem
127s Adding debian:Hongkong_Post_Root_CA_3.pem
127s Adding debian:ISRG_Root_X1.pem
127s Adding debian:ISRG_Root_X2.pem
127s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
127s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
127s Adding debian:Izenpe.com.pem
127s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
127s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
127s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
127s Adding debian:NAVER_Global_Root_Certification_Authority.pem
127s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
127s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
127s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
127s Adding debian:QuoVadis_Root_CA_1_G3.pem
127s Adding debian:QuoVadis_Root_CA_2.pem
127s Adding debian:QuoVadis_Root_CA_2_G3.pem
127s Adding debian:QuoVadis_Root_CA_3.pem
127s Adding debian:QuoVadis_Root_CA_3_G3.pem
127s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
127s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
127s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
127s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
127s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
127s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
127s Adding debian:SZAFIR_ROOT_CA2.pem
127s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
127s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
127s Adding debian:SecureSign_RootCA11.pem
127s Adding debian:SecureTrust_CA.pem
127s Adding debian:Secure_Global_CA.pem
127s Adding debian:Security_Communication_ECC_RootCA1.pem
127s Adding debian:Security_Communication_RootCA2.pem
127s Adding debian:Security_Communication_RootCA3.pem
127s Adding debian:Security_Communication_Root_CA.pem
127s Adding debian:Starfield_Class_2_CA.pem
127s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
127s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
127s Adding debian:SwissSign_Gold_CA_-_G2.pem
127s Adding debian:SwissSign_Silver_CA_-_G2.pem
127s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
127s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
127s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
127s Adding debian:TWCA_Global_Root_CA.pem
127s Adding debian:TWCA_Root_Certification_Authority.pem
127s Adding debian:TeliaSonera_Root_CA_v1.pem
127s Adding debian:Telia_Root_CA_v2.pem
127s Adding debian:TrustAsia_Global_Root_CA_G3.pem
127s Adding debian:TrustAsia_Global_Root_CA_G4.pem
127s Adding debian:Trustwave_Global_Certification_Authority.pem
127s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
127s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
127s Adding debian:TunTrust_Root_CA.pem
127s Adding debian:UCA_Extended_Validation_Root.pem
127s Adding debian:UCA_Global_G2_Root.pem
127s Adding debian:USERTrust_ECC_Certification_Authority.pem
127s Adding debian:USERTrust_RSA_Certification_Authority.pem
127s Adding debian:XRamp_Global_CA_Root.pem
127s Adding debian:certSIGN_ROOT_CA.pem
127s Adding debian:certSIGN_Root_CA_G2.pem
127s Adding debian:e-Szigno_Root_CA_2017.pem
127s Adding debian:ePKI_Root_Certification_Authority.pem
127s Adding debian:emSign_ECC_Root_CA_-_C3.pem
127s Adding debian:emSign_ECC_Root_CA_-_G3.pem
127s Adding debian:emSign_Root_CA_-_C1.pem
127s Adding debian:emSign_Root_CA_-_G1.pem
127s Adding debian:vTrus_ECC_Root_CA.pem
127s Adding debian:vTrus_Root_CA.pem
127s done.
127s Setting up default-jre-headless (2:1.21-76) ...
127s Setting up jaligner (1.0+dfsg-11) ...
127s Setting up mhap (2.1.3+dfsg-3) ...
127s Setting up canu (2.2+dfsg-5) ...
127s Setting up circlator (1.5.6-11) ...
128s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
128s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
128s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
128s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
128s Setting up autopkgtest-satdep (0) ...
132s (Reading database ... 77240 files and directories currently installed.)
132s Removing autopkgtest-satdep (0) ...
133s autopkgtest [11:33:14]: test run-unit-test: [-----------------------
133s + pkg=circlator
133s + export LC_ALL=C.UTF-8
133s + LC_ALL=C.UTF-8
133s + '[' /tmp/autopkgtest.WuCRGJ/autopkgtest_tmp = '' ']'
133s + cp -a /usr/share/doc/circlator/examples/assemble_test.py /usr/share/doc/circlator/examples/assembly_test.py /usr/share/doc/circlator/examples/bamfilter_test.py /usr/share/doc/circlator/examples/clean_test.py /usr/share/doc/circlator/examples/common_test.py /usr/share/doc/circlator/examples/data.tar.xz /usr/share/doc/circlator/examples/dnaa_test.py /usr/share/doc/circlator/examples/external_progs_test.py /usr/share/doc/circlator/examples/mapping_test.py /usr/share/doc/circlator/examples/merge_test.py /usr/share/doc/circlator/examples/minimus2_test.py /usr/share/doc/circlator/examples/start_fixer_test.py /tmp/autopkgtest.WuCRGJ/autopkgtest_tmp
133s + cd /tmp/autopkgtest.WuCRGJ/autopkgtest_tmp
133s + tar xaf data.tar.xz
133s + sed -i 's/data_dir = os.path.join(modules_dir, '\''tests'\'', '\''data'\'')/data_dir = os.path.join(os.getcwd(), '\''data'\'')/' ./assemble_test.py ./assembly_test.py ./bamfilter_test.py ./clean_test.py ./common_test.py ./dnaa_test.py ./external_progs_test.py ./mapping_test.py ./merge_test.py ./minimus2_test.py ./start_fixer_test.py
133s ++ py3versions --supported
133s + for py in $(py3versions --supported 2> /dev/null)
133s + eval dpkg-architecture --is amd64
133s ++ dpkg-architecture --is amd64
133s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
133s + python3.13 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
134s ============================= test session starts ==============================
134s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
134s cachedir: .pytest_cache
134s rootdir: /tmp/autopkgtest.WuCRGJ/autopkgtest_tmp
134s plugins: typeguard-4.4.1
134s collecting ... collected 0 items / 11 errors
134s 
134s ==================================== ERRORS ====================================
134s ______________________ ERROR collecting assemble_test.py _______________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/assemble_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s assemble_test.py:6: in <module>
134s     from circlator import assemble
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ______________________ ERROR collecting assembly_test.py _______________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/assembly_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s assembly_test.py:7: in <module>
134s     from circlator import assembly
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ______________________ ERROR collecting bamfilter_test.py ______________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/bamfilter_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s bamfilter_test.py:5: in <module>
134s     from circlator import bamfilter
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ________________________ ERROR collecting clean_test.py ________________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/clean_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s clean_test.py:5: in <module>
134s     from circlator import clean
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s _______________________ ERROR collecting common_test.py ________________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/common_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s common_test.py:3: in <module>
134s     from circlator import common
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ________________________ ERROR collecting dnaa_test.py _________________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/dnaa_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s dnaa_test.py:5: in <module>
134s     from circlator import dnaa
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ___________________ ERROR collecting external_progs_test.py ____________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/external_progs_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s external_progs_test.py:2: in <module>
134s     from circlator import external_progs
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s _______________________ ERROR collecting mapping_test.py _______________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/mapping_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s mapping_test.py:5: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ________________________ ERROR collecting merge_test.py ________________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/merge_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s merge_test.py:8: in <module>
134s     from circlator import merge
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s ______________________ ERROR collecting minimus2_test.py _______________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/minimus2_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s minimus2_test.py:6: in <module>
134s     from circlator import minimus2
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s _____________________ ERROR collecting start_fixer_test.py _____________________
134s ImportError while importing test module '/tmp/autopkgtest.WuCRGJ/autopkgtest_tmp/start_fixer_test.py'.
134s Hint: make sure your test modules/packages have valid Python names.
134s Traceback:
134s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
134s     return _bootstrap._gcd_import(name[level:], package, level)
134s start_fixer_test.py:9: in <module>
134s     from circlator import start_fixer
134s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
134s     from circlator import *
134s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
134s     import pysam
134s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
134s     from pysam.libchtslib import *
134s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
134s =============================== warnings summary ===============================
134s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
134s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
134s     __version__ = Distribution().from_name('pyfastaq').version
134s 
134s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
134s   /usr/lib/python3/dist-packages/circlator/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
134s     from pkg_resources import get_distribution
134s 
134s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
134s =========================== short test summary info ============================
134s ERROR assemble_test.py
134s ERROR assembly_test.py
134s ERROR bamfilter_test.py
134s ERROR clean_test.py
134s ERROR common_test.py
134s ERROR dnaa_test.py
134s ERROR external_progs_test.py
134s ERROR mapping_test.py
134s ERROR merge_test.py
134s ERROR minimus2_test.py
134s ERROR start_fixer_test.py
134s !!!!!!!!!!!!!!!!!!! Interrupted: 11 errors during collection !!!!!!!!!!!!!!!!!!!
134s ======================== 2 warnings, 11 errors in 0.63s ========================
135s autopkgtest [11:33:16]: test run-unit-test: -----------------------]
135s autopkgtest [11:33:16]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
135s run-unit-test        FAIL non-zero exit status 2
135s autopkgtest [11:33:16]: @@@@@@@@@@@@@@@@@@@@ summary
135s run-unit-test        FAIL non-zero exit status 2
147s nova [W] Using flock in prodstack6-ppc64el
147s Creating nova instance adt-plucky-ppc64el-circlator-20241113-110058-juju-7f2275-prod-proposed-migration-environment-20-6e979c26-b293-4f58-affd-6384b0786285 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...