0s autopkgtest [08:53:27]: starting date and time: 2024-11-13 08:53:27+0000
  0s autopkgtest [08:53:27]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [08:53:27]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tou2snhb/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-20.secgroup --name adt-plucky-arm64-circlator-20241113-085327-juju-7f2275-prod-proposed-migration-environment-20-a22a52ed-4ba8-4362-9825-432064f6f451 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 93s autopkgtest [08:55:00]: testbed dpkg architecture: arm64
 93s autopkgtest [08:55:00]: testbed apt version: 2.9.8
 93s autopkgtest [08:55:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 94s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 95s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 95s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 95s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
 95s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
 95s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
 95s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
 95s Fetched 1793 kB in 1s (1991 kB/s)
 95s Reading package lists...
 98s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
100s Calculating upgrade...
101s The following NEW packages will be installed:
101s   python3.13-gdbm
101s The following packages will be upgraded:
101s   libpython3-stdlib python3 python3-gdbm python3-minimal
101s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
101s Need to get 101 kB of archives.
101s After this operation, 141 kB of additional disk space will be used.
101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
101s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
101s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
101s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
101s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
102s Fetched 101 kB in 0s (282 kB/s)
102s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
102s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
102s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
102s Setting up python3-minimal (3.12.7-1) ...
102s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 79924 files and directories currently installed.)
102s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
102s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
102s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
102s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
103s Selecting previously unselected package python3.13-gdbm.
103s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
103s Unpacking python3.13-gdbm (3.13.0-2) ...
103s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
103s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
103s Setting up python3.13-gdbm (3.13.0-2) ...
103s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
103s Setting up python3 (3.12.7-1) ...
103s Setting up python3-gdbm:arm64 (3.12.7-1) ...
103s Processing triggers for man-db (2.12.1-3) ...
104s Reading package lists...
105s Building dependency tree...
105s Reading state information...
106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
106s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
108s Reading package lists...
108s Reading package lists...
109s Building dependency tree...
109s Reading state information...
110s Calculating upgrade...
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
111s Reading package lists...
111s Building dependency tree...
111s Reading state information...
113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
115s autopkgtest [08:55:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
116s autopkgtest [08:55:23]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
118s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (dsc) [1672 B]
118s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (tar) [5724 kB]
118s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (diff) [6152 B]
118s gpgv: Signature made Sat Dec  2 21:39:17 2023 UTC
118s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
118s gpgv: Can't check signature: No public key
118s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found
118s autopkgtest [08:55:25]: testing package circlator version 1.5.6-11
119s autopkgtest [08:55:26]: build not needed
121s autopkgtest [08:55:28]: test run-unit-test: preparing testbed
130s Reading package lists...
131s Building dependency tree...
131s Reading state information...
131s Starting pkgProblemResolver with broken count: 0
132s Starting 2 pkgProblemResolver with broken count: 0
132s Done
133s The following additional packages will be installed:
133s   aglfn binfmt-support bwa ca-certificates-java canu circlator
133s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
133s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
133s   jarwrapper java-common libaom3 libapache-pom-java
133s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
133s   libcommons-compress-java libcommons-io-java libcommons-parent-java
133s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
133s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
133s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
133s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
133s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
133s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
133s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0
133s   libsnappy1v5 libssw-java libthai-data libthai0 libtiff6 libwebp7 libwebpmux3
133s   libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap mummer
133s   openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
133s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
133s   python3-pluggy python3-pymummer python3-pysam python3-pytest python3.13
133s   python3.13-minimal samtools
133s Suggested packages:
133s   nanopolish default-jre gnuplot-doc libatinject-jsr330-api-java-doc
133s   libasm-java libxz-java libgd-tools libheif-plugin-x265
133s   libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
133s   libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar
133s   libheif-plugin-rav1e libheif-plugin-svtenc libjsr305-java-doc liblcms2-utils
133s   pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
133s   fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic
133s   python-lxml-doc python-openpyxl-doc python3.13-venv python3.13-doc cwltool
133s Recommended packages:
133s   spades fonts-liberation groff libheif-plugin-aomenc libcups2t64
133s   libasound2t64 python3-bs4 python3-cssselect python3-html5lib python3-pil
133s The following NEW packages will be installed:
133s   aglfn autopkgtest-satdep binfmt-support bwa ca-certificates-java canu
133s   circlator default-jre-headless fastaq fastjar fontconfig fontconfig-config
133s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
133s   jarwrapper java-common libaom3 libapache-pom-java
133s   libatinject-jsr330-api-java libcairo2 libcommons-codec-java
133s   libcommons-compress-java libcommons-io-java libcommons-parent-java
133s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
133s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
133s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
133s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
133s   libjpeg8 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0 libpango-1.0-0
133s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1 libpixman-1-0
133s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0
133s   libsnappy1v5 libssw-java libthai-data libthai0 libtiff6 libwebp7 libwebpmux3
133s   libxcb-render0 libxcb-shm0 libxpm4 libxrender1 libxslt1.1 mhap mummer
133s   openjdk-21-jre-headless prodigal python3-all python3-et-xmlfile
133s   python3-iniconfig python3-lxml python3-openpyxl python3-packaging
133s   python3-pluggy python3-pymummer python3-pysam python3-pytest python3.13
133s   python3.13-minimal samtools
133s 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded.
133s Need to get 99.1 MB/99.1 MB of archives.
133s After this operation, 372 MB of additional disk space will be used.
133s Get:1 /tmp/autopkgtest.QgmUEZ/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
133s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 binfmt-support arm64 2.2.2-7 [55.9 kB]
134s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB]
134s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB]
134s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 bwa arm64 0.7.18-1 [201 kB]
134s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 ca-certificates-java all 20240118 [11.6 kB]
134s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
134s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libsnappy1v5 arm64 1.2.1-1 [30.4 kB]
134s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfilesys-df-perl arm64 0.92-7build5 [11.0 kB]
134s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 java-common all 0.76 [6852 B]
134s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
134s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
134s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
134s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcsclite1 arm64 2.3.0-1 [24.4 kB]
134s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [45.7 MB]
135s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 default-jre-headless arm64 2:1.21-76 [3176 B]
135s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastjar arm64 2:0.98-7 [61.9 kB]
135s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 jarwrapper all 0.80 [9800 B]
135s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 libapache-pom-java all 33-2 [5874 B]
135s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-parent-java all 56-1 [10.7 kB]
135s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-codec-java all 1.17.1-1 [302 kB]
135s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-io-java all 2.17.0-1 [457 kB]
135s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcommons-compress-java all 1.27.1-2 [610 kB]
135s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
136s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
136s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 liberror-prone-java all 2.18.0-1 [22.5 kB]
136s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
136s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 libguava-java all 32.0.1-1 [2692 kB]
136s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 jaligner all 1.0+dfsg-11 [136 kB]
136s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw-java arm64 1.1-15 [18.6 kB]
136s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 mhap all 2.1.3+dfsg-3 [160 kB]
136s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
136s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
136s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
136s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
136s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
136s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
136s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
136s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
136s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
136s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
136s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
136s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
136s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libaom3 arm64 3.11.0~rc1-1 [1837 kB]
136s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-aomdec arm64 1.18.1-2 [10.9 kB]
136s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libde265-0 arm64 1.0.15-1build4 [146 kB]
136s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif-plugin-libde265 arm64 1.18.1-2 [8612 B]
136s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libheif1 arm64 1.18.1-2 [274 kB]
136s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
136s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
136s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
136s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB]
136s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
136s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
136s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
136s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
136s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
136s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libxpm4 arm64 1:3.5.17-1build2 [35.1 kB]
136s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libgd3 arm64 2.3.3-12ubuntu3 [122 kB]
136s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblua5.4-0 arm64 5.4.6-3build2 [158 kB]
136s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB]
136s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
136s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
136s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
136s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [234 kB]
136s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [48.9 kB]
136s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [27.5 kB]
136s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB]
136s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 gnuplot-nox arm64 6.0.0+dfsg1-1ubuntu3 [956 kB]
136s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 canu arm64 2.2+dfsg-5 [1500 kB]
136s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB]
136s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB]
136s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.20-3 [590 kB]
136s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastaq all 3.17.0-8 [48.2 kB]
136s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-et-xmlfile all 2.0.0-1 [79.4 kB]
136s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB]
136s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB]
136s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
136s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB]
137s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB]
137s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymummer all 0.11.0-4 [17.1 kB]
137s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB]
137s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB]
137s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 circlator all 1.5.6-11 [4618 kB]
137s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB]
137s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB]
137s Get:87 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B]
137s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B]
137s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB]
137s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB]
138s Fetched 99.1 MB in 4s (27.0 MB/s)
138s Selecting previously unselected package binfmt-support.
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138s Preparing to unpack .../00-binfmt-support_2.2.2-7_arm64.deb ...
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138s Selecting previously unselected package libpython3.13-minimal:arm64.
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142s Selecting previously unselected package fonts-dejavu-mono.
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142s Selecting previously unselected package fontconfig-config.
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142s Selecting previously unselected package libpixman-1-0:arm64.
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144s Selecting previously unselected package libdatrie1:arm64.
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144s Selecting previously unselected package libpango-1.0-0:arm64.
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147s Setting up libhtscodecs2:arm64 (1.6.1-1) ...
147s Setting up fastjar (2:0.98-7) ...
147s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
147s Setting up liblcms2-2:arm64 (2.16-2) ...
147s Setting up python3-iniconfig (1.1.1-2) ...
147s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
147s Setting up libfastutil-java (8.5.15+dfsg-1) ...
147s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
147s Setting up libaom3:arm64 (3.11.0~rc1-1) ...
147s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
147s Setting up libjsr305-java (0.1~+svn49-11) ...
147s Setting up libxpm4:arm64 (1:3.5.17-1build2) ...
147s Setting up java-common (0.76) ...
147s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
147s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
147s Setting up libxcb-render0:arm64 (1.17.0-2) ...
147s Setting up prodigal (1:2.6.3-6) ...
147s Setting up bwa (0.7.18-1) ...
147s Setting up libfilesys-df-perl (0.92-7build5) ...
147s Setting up libdeflate0:arm64 (1.22-1) ...
147s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
147s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
147s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
147s Setting up libssw-java (1.1-15) ...
147s Setting up libsnappy1v5:arm64 (1.2.1-1) ...
147s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ...
147s Setting up python3-packaging (24.1-1) ...
148s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
148s Setting up libapache-pom-java (33-2) ...
148s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
148s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
148s Setting up fonts-dejavu-mono (2.37-8) ...
148s Setting up binfmt-support (2.2.2-7) ...
148s update-binfmts: warning: python3.12 already enabled in kernel.
148s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

149s Setting up fonts-dejavu-core (2.37-8) ...
149s Setting up libpcsclite1:arm64 (2.3.0-1) ...
149s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
149s Setting up python3-pluggy (1.5.0-1) ...
149s Setting up libwebp7:arm64 (1.4.0-0.1) ...
149s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ...
149s Setting up mummer (3.23+dfsg-8) ...
149s Setting up python3-et-xmlfile (2.0.0-1) ...
150s Setting up libhts3t64:arm64 (1.20+ds-1) ...
150s Setting up liblua5.4-0:arm64 (5.4.6-3build2) ...
150s Setting up python3.13-minimal (3.13.0-2) ...
151s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
151s Setting up libthai-data (0.1.29-2build1) ...
151s Setting up ca-certificates-java (20240118) ...
151s No JRE found. Skipping Java certificates setup.
151s Setting up libde265-0:arm64 (1.0.15-1build4) ...
151s Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
151s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ...
151s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
151s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
151s Setting up python3-pysam (0.22.1+ds-2) ...
152s Setting up openjdk-21-jre-headless:arm64 (21.0.5+11-1) ...
152s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode
152s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
152s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
152s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
152s update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
152s Setting up jarwrapper (0.80) ...
152s Setting up python3.13 (3.13.0-2) ...
154s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
154s Setting up python3-pytest (8.3.3-1) ...
155s Setting up libcommons-parent-java (56-1) ...
155s Setting up python3-all (3.12.7-1) ...
155s Setting up samtools (1.20-3) ...
155s Setting up libthai0:arm64 (0.1.29-2build1) ...
155s Setting up libraqm0:arm64 (0.10.1-1build1) ...
155s Setting up python3-lxml:arm64 (5.3.0-1) ...
156s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
156s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
156s Setting up libcommons-codec-java (1.17.1-1) ...
156s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
158s Regenerating fonts cache... done.
158s Setting up libcommons-io-java (2.17.0-1) ...
158s Setting up fastaq (3.17.0-8) ...
158s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
158s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
158s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
158s   gbk_regex = re.compile('^LOCUS\s+\S')
158s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
158s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
158s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
158s   gbk_regex = re.compile('^LOCUS\s+\S')
158s Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ...
158s Setting up libcairo2:arm64 (1.18.2-2) ...
158s Setting up python3-pymummer (0.11.0-4) ...
159s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
160s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ...
160s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ...
160s Setting up libcommons-compress-java (1.27.1-2) ...
160s Setting up libheif-plugin-aomdec:arm64 (1.18.1-2) ...
160s Setting up libheif-plugin-libde265:arm64 (1.18.1-2) ...
160s Setting up liberror-prone-java (2.18.0-1) ...
160s Setting up libheif1:arm64 (1.18.1-2) ...
160s Setting up libguava-java (32.0.1-1) ...
160s Setting up libgd3:arm64 (2.3.3-12ubuntu3) ...
160s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
160s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
160s Processing triggers for install-info (7.1.1-1) ...
160s Processing triggers for libc-bin (2.40-1ubuntu3) ...
160s Processing triggers for systemd (256.5-2ubuntu4) ...
160s Processing triggers for man-db (2.12.1-3) ...
161s Processing triggers for ca-certificates-java (20240118) ...
162s Adding debian:ACCVRAIZ1.pem
162s Adding debian:AC_RAIZ_FNMT-RCM.pem
162s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
162s Adding debian:ANF_Secure_Server_Root_CA.pem
162s Adding debian:Actalis_Authentication_Root_CA.pem
162s Adding debian:AffirmTrust_Commercial.pem
162s Adding debian:AffirmTrust_Networking.pem
162s Adding debian:AffirmTrust_Premium.pem
162s Adding debian:AffirmTrust_Premium_ECC.pem
162s Adding debian:Amazon_Root_CA_1.pem
162s Adding debian:Amazon_Root_CA_2.pem
162s Adding debian:Amazon_Root_CA_3.pem
162s Adding debian:Amazon_Root_CA_4.pem
162s Adding debian:Atos_TrustedRoot_2011.pem
162s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
162s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
162s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
162s Adding debian:BJCA_Global_Root_CA1.pem
162s Adding debian:BJCA_Global_Root_CA2.pem
162s Adding debian:Baltimore_CyberTrust_Root.pem
162s Adding debian:Buypass_Class_2_Root_CA.pem
162s Adding debian:Buypass_Class_3_Root_CA.pem
162s Adding debian:CA_Disig_Root_R2.pem
162s Adding debian:CFCA_EV_ROOT.pem
162s Adding debian:COMODO_Certification_Authority.pem
162s Adding debian:COMODO_ECC_Certification_Authority.pem
162s Adding debian:COMODO_RSA_Certification_Authority.pem
162s Adding debian:Certainly_Root_E1.pem
162s Adding debian:Certainly_Root_R1.pem
162s Adding debian:Certigna.pem
162s Adding debian:Certigna_Root_CA.pem
162s Adding debian:Certum_EC-384_CA.pem
162s Adding debian:Certum_Trusted_Network_CA.pem
162s Adding debian:Certum_Trusted_Network_CA_2.pem
162s Adding debian:Certum_Trusted_Root_CA.pem
162s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
162s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
162s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
162s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
162s Adding debian:Comodo_AAA_Services_root.pem
162s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
162s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
162s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
162s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
162s Adding debian:DigiCert_Assured_ID_Root_CA.pem
162s Adding debian:DigiCert_Assured_ID_Root_G2.pem
162s Adding debian:DigiCert_Assured_ID_Root_G3.pem
162s Adding debian:DigiCert_Global_Root_CA.pem
162s Adding debian:DigiCert_Global_Root_G2.pem
162s Adding debian:DigiCert_Global_Root_G3.pem
162s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
162s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
162s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
162s Adding debian:DigiCert_Trusted_Root_G4.pem
162s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
162s Adding debian:Entrust_Root_Certification_Authority.pem
162s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
162s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
162s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
162s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
162s Adding debian:GLOBALTRUST_2020.pem
162s Adding debian:GTS_Root_R1.pem
162s Adding debian:GTS_Root_R2.pem
162s Adding debian:GTS_Root_R3.pem
162s Adding debian:GTS_Root_R4.pem
162s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
162s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
162s Adding debian:GlobalSign_Root_CA.pem
162s Adding debian:GlobalSign_Root_CA_-_R3.pem
162s Adding debian:GlobalSign_Root_CA_-_R6.pem
162s Adding debian:GlobalSign_Root_E46.pem
162s Adding debian:GlobalSign_Root_R46.pem
162s Adding debian:Go_Daddy_Class_2_CA.pem
162s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
162s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
162s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
162s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
162s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
162s Adding debian:HiPKI_Root_CA_-_G1.pem
162s Adding debian:Hongkong_Post_Root_CA_3.pem
162s Adding debian:ISRG_Root_X1.pem
162s Adding debian:ISRG_Root_X2.pem
162s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
162s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
162s Adding debian:Izenpe.com.pem
162s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
162s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
162s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
162s Adding debian:NAVER_Global_Root_Certification_Authority.pem
162s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
162s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
162s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
162s Adding debian:QuoVadis_Root_CA_1_G3.pem
162s Adding debian:QuoVadis_Root_CA_2.pem
162s Adding debian:QuoVadis_Root_CA_2_G3.pem
162s Adding debian:QuoVadis_Root_CA_3.pem
162s Adding debian:QuoVadis_Root_CA_3_G3.pem
162s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
162s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
162s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
162s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
162s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
162s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
162s Adding debian:SZAFIR_ROOT_CA2.pem
162s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
162s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
162s Adding debian:SecureSign_RootCA11.pem
162s Adding debian:SecureTrust_CA.pem
162s Adding debian:Secure_Global_CA.pem
162s Adding debian:Security_Communication_ECC_RootCA1.pem
162s Adding debian:Security_Communication_RootCA2.pem
162s Adding debian:Security_Communication_RootCA3.pem
162s Adding debian:Security_Communication_Root_CA.pem
162s Adding debian:Starfield_Class_2_CA.pem
162s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
162s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
162s Adding debian:SwissSign_Gold_CA_-_G2.pem
162s Adding debian:SwissSign_Silver_CA_-_G2.pem
162s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
162s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
162s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
162s Adding debian:TWCA_Global_Root_CA.pem
162s Adding debian:TWCA_Root_Certification_Authority.pem
162s Adding debian:TeliaSonera_Root_CA_v1.pem
162s Adding debian:Telia_Root_CA_v2.pem
162s Adding debian:TrustAsia_Global_Root_CA_G3.pem
162s Adding debian:TrustAsia_Global_Root_CA_G4.pem
163s Adding debian:Trustwave_Global_Certification_Authority.pem
163s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
163s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
163s Adding debian:TunTrust_Root_CA.pem
163s Adding debian:UCA_Extended_Validation_Root.pem
163s Adding debian:UCA_Global_G2_Root.pem
163s Adding debian:USERTrust_ECC_Certification_Authority.pem
163s Adding debian:USERTrust_RSA_Certification_Authority.pem
163s Adding debian:XRamp_Global_CA_Root.pem
163s Adding debian:certSIGN_ROOT_CA.pem
163s Adding debian:certSIGN_Root_CA_G2.pem
163s Adding debian:e-Szigno_Root_CA_2017.pem
163s Adding debian:ePKI_Root_Certification_Authority.pem
163s Adding debian:emSign_ECC_Root_CA_-_C3.pem
163s Adding debian:emSign_ECC_Root_CA_-_G3.pem
163s Adding debian:emSign_Root_CA_-_C1.pem
163s Adding debian:emSign_Root_CA_-_G1.pem
163s Adding debian:vTrus_ECC_Root_CA.pem
163s Adding debian:vTrus_Root_CA.pem
163s done.
163s Setting up default-jre-headless (2:1.21-76) ...
163s Setting up jaligner (1.0+dfsg-11) ...
163s Setting up mhap (2.1.3+dfsg-3) ...
163s Setting up canu (2.2+dfsg-5) ...
163s Setting up circlator (1.5.6-11) ...
163s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
163s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
163s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
163s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
163s Setting up autopkgtest-satdep (0) ...
169s (Reading database ... 83403 files and directories currently installed.)
169s Removing autopkgtest-satdep (0) ...
170s autopkgtest [08:56:17]: test run-unit-test: [-----------------------
170s + pkg=circlator
170s + export LC_ALL=C.UTF-8
170s + LC_ALL=C.UTF-8
170s + '[' /tmp/autopkgtest.QgmUEZ/autopkgtest_tmp = '' ']'
170s + 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.QgmUEZ/autopkgtest_tmp
170s + cd /tmp/autopkgtest.QgmUEZ/autopkgtest_tmp
170s + tar xaf data.tar.xz
171s + 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
171s ++ py3versions --supported
171s + for py in $(py3versions --supported 2> /dev/null)
171s + eval dpkg-architecture --is amd64
171s ++ dpkg-architecture --is amd64
171s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
171s + python3.13 -m pytest -v -k 'not (test_build_spades_kmers or test_make_spades_command)'
171s ============================= test session starts ==============================
171s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
171s cachedir: .pytest_cache
171s rootdir: /tmp/autopkgtest.QgmUEZ/autopkgtest_tmp
171s plugins: typeguard-4.4.1
172s collecting ... collected 0 items / 11 errors
172s 
172s ==================================== ERRORS ====================================
172s ______________________ ERROR collecting assemble_test.py _______________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/assemble_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s assemble_test.py:6: in <module>
172s     from circlator import assemble
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ______________________ ERROR collecting assembly_test.py _______________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/assembly_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s assembly_test.py:7: in <module>
172s     from circlator import assembly
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ______________________ ERROR collecting bamfilter_test.py ______________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/bamfilter_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s bamfilter_test.py:5: in <module>
172s     from circlator import bamfilter
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ________________________ ERROR collecting clean_test.py ________________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/clean_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s clean_test.py:5: in <module>
172s     from circlator import clean
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s _______________________ ERROR collecting common_test.py ________________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/common_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s common_test.py:3: in <module>
172s     from circlator import common
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ________________________ ERROR collecting dnaa_test.py _________________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/dnaa_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s dnaa_test.py:5: in <module>
172s     from circlator import dnaa
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ___________________ ERROR collecting external_progs_test.py ____________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/external_progs_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s external_progs_test.py:2: in <module>
172s     from circlator import external_progs
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s _______________________ ERROR collecting mapping_test.py _______________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/mapping_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s mapping_test.py:5: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ________________________ ERROR collecting merge_test.py ________________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/merge_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s merge_test.py:8: in <module>
172s     from circlator import merge
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s ______________________ ERROR collecting minimus2_test.py _______________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/minimus2_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s minimus2_test.py:6: in <module>
172s     from circlator import minimus2
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s _____________________ ERROR collecting start_fixer_test.py _____________________
172s ImportError while importing test module '/tmp/autopkgtest.QgmUEZ/autopkgtest_tmp/start_fixer_test.py'.
172s Hint: make sure your test modules/packages have valid Python names.
172s Traceback:
172s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
172s     return _bootstrap._gcd_import(name[level:], package, level)
172s start_fixer_test.py:9: in <module>
172s     from circlator import start_fixer
172s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
172s     from circlator import *
172s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
172s     import pysam
172s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
172s     from pysam.libchtslib import *
172s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
172s =============================== warnings summary ===============================
172s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
172s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
172s     __version__ = Distribution().from_name('pyfastaq').version
172s 
172s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
172s   /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
172s     from pkg_resources import get_distribution
172s 
172s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
172s =========================== short test summary info ============================
172s ERROR assemble_test.py
172s ERROR assembly_test.py
172s ERROR bamfilter_test.py
172s ERROR clean_test.py
172s ERROR common_test.py
172s ERROR dnaa_test.py
172s ERROR external_progs_test.py
172s ERROR mapping_test.py
172s ERROR merge_test.py
172s ERROR minimus2_test.py
172s ERROR start_fixer_test.py
172s !!!!!!!!!!!!!!!!!!! Interrupted: 11 errors during collection !!!!!!!!!!!!!!!!!!!
172s ======================== 2 warnings, 11 errors in 0.76s ========================
172s autopkgtest [08:56:19]: test run-unit-test: -----------------------]
173s run-unit-test        FAIL non-zero exit status 2
173s autopkgtest [08:56:20]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
173s autopkgtest [08:56:20]: @@@@@@@@@@@@@@@@@@@@ summary
173s run-unit-test        FAIL non-zero exit status 2
212s nova [W] Skipping flock in bos03-arm64
212s Creating nova instance adt-plucky-arm64-circlator-20241113-085327-juju-7f2275-prod-proposed-migration-environment-20-a22a52ed-4ba8-4362-9825-432064f6f451 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...