0s autopkgtest [08:11:18]: starting date and time: 2024-11-13 08:11:18+0000
  0s autopkgtest [08:11:18]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [08:11:18]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9grl_9_7/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-30.secgroup --name adt-plucky-amd64-circlator-20241113-081118-juju-7f2275-prod-proposed-migration-environment-15-2b00bd27-8425-48c0-a1d0-63d3b2200bca --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/
 47s autopkgtest [08:12:05]: testbed dpkg architecture: amd64
 47s autopkgtest [08:12:05]: testbed apt version: 2.9.8
 47s autopkgtest [08:12:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 48s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 48s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 48s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB]
 48s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 48s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 48s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB]
 48s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB]
 48s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB]
 48s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB]
 48s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB]
 48s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB]
 48s Fetched 2171 kB in 1s (2636 kB/s)
 48s Reading package lists...
 51s Reading package lists...
 51s Building dependency tree...
 51s Reading state information...
 51s Calculating upgrade...
 51s The following NEW packages will be installed:
 51s   python3.13-gdbm
 51s The following packages will be upgraded:
 51s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
 52s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 52s Need to get 253 kB of archives.
 52s After this operation, 147 kB of additional disk space will be used.
 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 52s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 52s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 52s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 52s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 52s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB]
 52s Fetched 253 kB in 0s (598 kB/s)
 52s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75541 files and directories currently installed.)
 52s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 52s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 52s Setting up python3-minimal (3.12.7-1) ...
 53s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75541 files and directories currently installed.)
 53s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 53s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 53s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 53s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 53s Selecting previously unselected package python3.13-gdbm.
 53s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
 53s Unpacking python3.13-gdbm (3.13.0-2) ...
 53s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
 53s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 53s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ...
 53s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
 53s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ...
 53s Setting up python3.13-gdbm (3.13.0-2) ...
 53s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 53s Setting up python3 (3.12.7-1) ...
 53s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 53s Processing triggers for man-db (2.12.1-3) ...
 53s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 54s Reading package lists...
 54s Building dependency tree...
 54s Reading state information...
 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 55s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 55s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 55s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 55s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 56s Reading package lists...
 56s Reading package lists...
 56s Building dependency tree...
 56s Reading state information...
 56s Calculating upgrade...
 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 56s Reading package lists...
 56s Building dependency tree...
 56s Reading state information...
 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 59s autopkgtest [08:12:17]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 59s autopkgtest [08:12:17]: @@@@@@@@@@@@@@@@@@@@ apt-source circlator
 61s Get:1 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (dsc) [1672 B]
 61s Get:2 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (tar) [5724 kB]
 61s Get:3 http://ftpmaster.internal/ubuntu plucky/universe circlator 1.5.6-11 (diff) [6152 B]
 61s gpgv: Signature made Sat Dec  2 21:39:17 2023 UTC
 61s gpgv:                using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
 61s gpgv: Can't check signature: No public key
 61s dpkg-source: warning: cannot verify inline signature for ./circlator_1.5.6-11.dsc: no acceptable signature found
 61s autopkgtest [08:12:19]: testing package circlator version 1.5.6-11
 62s autopkgtest [08:12:20]: build not needed
 63s autopkgtest [08:12:21]: test run-unit-test: preparing testbed
 64s Reading package lists...
 64s Building dependency tree...
 64s Reading state information...
 64s Starting pkgProblemResolver with broken count: 0
 64s Starting 2 pkgProblemResolver with broken count: 0
 64s Done
 64s The following additional packages will be installed:
 64s   aglfn bamtools binfmt-support bwa ca-certificates-java canu circlator
 64s   default-jre-headless fastaq fastjar fontconfig fontconfig-config
 64s   fonts-dejavu-core fonts-dejavu-mono gnuplot-data gnuplot-nox jaligner
 64s   jarwrapper java-common libaom3 libapache-pom-java
 64s   libatinject-jsr330-api-java libbamtools2.5.2 libcairo2 libcommons-codec-java
 64s   libcommons-compress-java libcommons-io-java libcommons-parent-java
 64s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
 64s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
 64s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
 64s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
 64s   libjpeg8 libjsoncpp26 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0
 64s   libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1
 64s   libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0
 64s   libsharpyuv0 libsnappy1v5 libssw-java libssw0 libthai-data libthai0 libtiff6
 64s   libwebp7 libwebpmux3 libxcb-render0 libxcb-shm0 libxpm4 libxrender1
 64s   libxslt1.1 mhap mummer openjdk-21-jre-headless prodigal python3-all
 64s   python3-et-xmlfile python3-iniconfig python3-joblib python3-lxml
 64s   python3-openpyxl python3-packaging python3-pluggy python3-pymummer
 64s   python3-pysam python3-pytest python3.13 python3.13-minimal samtools spades
 64s Suggested packages:
 64s   nanopolish default-jre gnuplot-doc libatinject-jsr330-api-java-doc
 64s   libasm-java libxz-java libgd-tools libheif-plugin-x265
 64s   libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc
 64s   libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar
 64s   libheif-plugin-rav1e libheif-plugin-svtenc libjsr305-java-doc liblcms2-utils
 64s   pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic
 64s   fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic
 64s   python-joblib-doc python-lxml-doc python-openpyxl-doc python3.13-venv
 64s   python3.13-doc cwltool
 64s Recommended packages:
 64s   fonts-liberation groff libheif-plugin-aomenc libcups2t64 libasound2t64
 64s   python3-numpy python3-simplejson python3-psutil python3-bs4
 64s   python3-cssselect python3-html5lib python3-pil
 65s The following NEW packages will be installed:
 65s   aglfn autopkgtest-satdep bamtools binfmt-support bwa ca-certificates-java
 65s   canu circlator default-jre-headless fastaq fastjar fontconfig
 65s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono gnuplot-data
 65s   gnuplot-nox jaligner jarwrapper java-common libaom3 libapache-pom-java
 65s   libatinject-jsr330-api-java libbamtools2.5.2 libcairo2 libcommons-codec-java
 65s   libcommons-compress-java libcommons-io-java libcommons-parent-java
 65s   libdatrie1 libde265-0 libdeflate0 liberror-prone-java libfastutil-java
 65s   libfilesys-df-perl libfontconfig1 libgd3 libgomp1 libgraphite2-3
 65s   libguava-java libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265
 65s   libheif1 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8
 65s   libjpeg8 libjsoncpp26 libjsr305-java liblcms2-2 liblerc4 liblua5.4-0
 65s   libnlopt0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpcsclite1
 65s   libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib libraqm0
 65s   libsharpyuv0 libsnappy1v5 libssw-java libssw0 libthai-data libthai0 libtiff6
 65s   libwebp7 libwebpmux3 libxcb-render0 libxcb-shm0 libxpm4 libxrender1
 65s   libxslt1.1 mhap mummer openjdk-21-jre-headless prodigal python3-all
 65s   python3-et-xmlfile python3-iniconfig python3-joblib python3-lxml
 65s   python3-openpyxl python3-packaging python3-pluggy python3-pymummer
 65s   python3-pysam python3-pytest python3.13 python3.13-minimal samtools spades
 65s 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded.
 65s Need to get 111 MB/111 MB of archives.
 65s After this operation, 414 MB of additional disk space will be used.
 65s Get:1 /tmp/autopkgtest.CKTTLW/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [732 B]
 65s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 binfmt-support amd64 2.2.2-7 [56.2 kB]
 65s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
 65s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
 65s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6build1 [144 kB]
 65s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libjsoncpp26 amd64 1.9.6-2 [89.9 kB]
 65s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 bamtools amd64 2.5.2+dfsg-6build1 [178 kB]
 65s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 bwa amd64 0.7.18-1 [204 kB]
 65s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 ca-certificates-java all 20240118 [11.6 kB]
 65s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 65s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB]
 65s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfilesys-df-perl amd64 0.92-7build5 [11.4 kB]
 65s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 java-common all 0.76 [6852 B]
 65s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 65s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
 65s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 65s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcsclite1 amd64 2.3.0-1 [23.9 kB]
 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [46.4 MB]
 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 default-jre-headless amd64 2:1.21-76 [3178 B]
 66s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastjar amd64 2:0.98-7 [67.1 kB]
 66s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 jarwrapper all 0.80 [9800 B]
 66s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libapache-pom-java all 33-2 [5874 B]
 66s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
 66s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-codec-java all 1.17.1-1 [302 kB]
 66s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-io-java all 2.17.0-1 [457 kB]
 66s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcommons-compress-java all 1.27.1-2 [610 kB]
 66s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfastutil-java all 8.5.15+dfsg-1 [20.2 MB]
 67s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
 67s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
 67s Get:30 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
 67s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
 67s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 jaligner all 1.0+dfsg-11 [136 kB]
 67s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw-java amd64 1.1-15 [18.9 kB]
 67s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 mhap all 2.1.3+dfsg-3 [160 kB]
 67s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB]
 67s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB]
 67s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 67s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 67s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 67s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 68s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
 68s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
 68s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
 68s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 68s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
 68s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
 68s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libaom3 amd64 3.11.0~rc1-1 [2762 kB]
 68s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-aomdec amd64 1.18.1-2 [11.1 kB]
 68s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libde265-0 amd64 1.0.15-1build4 [168 kB]
 68s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif-plugin-libde265 amd64 1.18.1-2 [8758 B]
 68s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libheif1 amd64 1.18.1-2 [293 kB]
 68s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
 68s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 68s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
 68s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
 68s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 68s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 68s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
 68s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
 68s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
 68s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB]
 68s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libgd3 amd64 2.3.3-12ubuntu3 [127 kB]
 68s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.6-3build2 [166 kB]
 68s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
 68s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
 68s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
 68s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
 68s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB]
 68s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB]
 68s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB]
 68s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
 68s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 gnuplot-nox amd64 6.0.0+dfsg1-1ubuntu3 [989 kB]
 68s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 canu amd64 2.2+dfsg-5 [1536 kB]
 68s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
 68s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
 68s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 samtools amd64 1.20-3 [599 kB]
 68s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 fastaq all 3.17.0-8 [48.2 kB]
 68s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-et-xmlfile all 2.0.0-1 [79.4 kB]
 68s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB]
 68s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB]
 68s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openpyxl all 3.1.5+dfsg-1 [152 kB]
 68s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB]
 68s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB]
 68s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymummer all 0.11.0-4 [17.1 kB]
 68s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
 68s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 prodigal amd64 1:2.6.3-6 [643 kB]
 68s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 circlator all 1.5.6-11 [4618 kB]
 69s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
 69s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 libssw0 amd64 1.1-15 [22.5 kB]
 69s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
 69s Get:91 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
 69s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
 69s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB]
 69s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
 69s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB]
 69s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnlopt0 amd64 2.7.1-5ubuntu1 [183 kB]
 69s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 spades amd64 3.15.5+dfsg-7 [9133 kB]
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 74s Unpacking python3-pluggy (1.5.0-1) ...
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 74s Unpacking python3-pytest (8.3.3-1) ...
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 74s Unpacking spades (3.15.5+dfsg-7) ...
 74s Selecting previously unselected package autopkgtest-satdep.
 74s Preparing to unpack .../96-1-autopkgtest-satdep.deb ...
 74s Unpacking autopkgtest-satdep (0) ...
 74s Setting up libhtscodecs2:amd64 (1.6.1-1) ...
 74s Setting up fastjar (2:0.98-7) ...
 74s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
 74s Setting up liblcms2-2:amd64 (2.16-2) ...
 74s Setting up python3-iniconfig (1.1.1-2) ...
 74s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
 74s Setting up libfastutil-java (8.5.15+dfsg-1) ...
 74s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
 74s Setting up libaom3:amd64 (3.11.0~rc1-1) ...
 74s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
 74s Setting up libjsr305-java (0.1~+svn49-11) ...
 74s Setting up libxpm4:amd64 (1:3.5.17-1build2) ...
 74s Setting up java-common (0.76) ...
 74s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
 74s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
 74s Setting up python3-joblib (1.3.2-5) ...
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 74s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ...
 74s Setting up python3-packaging (24.1-1) ...
 75s Setting up libjsoncpp26:amd64 (1.9.6-2) ...
 75s Setting up aglfn (1.7+git20191031.4036a9c-2) ...
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 75s Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
 75s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
 75s Setting up fonts-dejavu-mono (2.37-8) ...
 75s Setting up binfmt-support (2.2.2-7) ...
 75s update-binfmts: warning: python3.12 already enabled in kernel.
 75s Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.

 75s Setting up fonts-dejavu-core (2.37-8) ...
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 75s Setting up python3-pluggy (1.5.0-1) ...
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 76s Setting up libharfbuzz0b:amd64 (10.0.1-1) ...
 76s Setting up libthai-data (0.1.29-2build1) ...
 76s Setting up ca-certificates-java (20240118) ...
 76s No JRE found. Skipping Java certificates setup.
 76s Setting up libde265-0:amd64 (1.0.15-1build4) ...
 76s Setting up libwebpmux3:amd64 (1.4.0-0.1) ...
 76s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ...
 76s Setting up libssw0:amd64 (1.1-15) ...
 76s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
 76s Setting up gnuplot-data (6.0.0+dfsg1-1ubuntu3) ...
 76s Setting up python3-pysam (0.22.1+ds-2) ...
 76s Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ...
 76s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
 76s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
 76s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
 76s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
 76s update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
 76s Setting up jarwrapper (0.80) ...
 76s Setting up python3.13 (3.13.0-2) ...
 77s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
 77s Setting up python3-pytest (8.3.3-1) ...
 78s Setting up libcommons-parent-java (56-1) ...
 78s Setting up python3-all (3.12.7-1) ...
 78s Setting up samtools (1.20-3) ...
 78s Setting up libthai0:amd64 (0.1.29-2build1) ...
 78s Setting up libraqm0:amd64 (0.10.1-1build1) ...
 78s Setting up python3-lxml:amd64 (5.3.0-1) ...
 78s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
 78s Setting up spades (3.15.5+dfsg-7) ...
 78s /usr/share/spades/spades_pipeline/support.py:531: SyntaxWarning: invalid escape sequence '\d'
 78s   return [atoi(c) for c in re.split("(\d+)", text)]
 78s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
 78s Setting up libcommons-codec-java (1.17.1-1) ...
 78s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
 80s Regenerating fonts cache... done.
 80s Setting up libcommons-io-java (2.17.0-1) ...
 80s Setting up fastaq (3.17.0-8) ...
 80s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
 80s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
 80s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
 80s   gbk_regex = re.compile('^LOCUS\s+\S')
 80s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s'
 80s   phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$')
 80s /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s'
 80s   gbk_regex = re.compile('^LOCUS\s+\S')
 80s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ...
 80s Setting up libcairo2:amd64 (1.18.2-2) ...
 80s Setting up python3-pymummer (0.11.0-4) ...
 81s Setting up python3-openpyxl (3.1.5+dfsg-1) ...
 81s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ...
 81s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ...
 81s Setting up libcommons-compress-java (1.27.1-2) ...
 81s Setting up libheif-plugin-aomdec:amd64 (1.18.1-2) ...
 81s Setting up libheif-plugin-libde265:amd64 (1.18.1-2) ...
 81s Setting up liberror-prone-java (2.18.0-1) ...
 81s Setting up libheif1:amd64 (1.18.1-2) ...
 81s Setting up libguava-java (32.0.1-1) ...
 81s Setting up libgd3:amd64 (2.3.3-12ubuntu3) ...
 81s Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ...
 81s update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode
 81s Processing triggers for install-info (7.1.1-1) ...
 81s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 81s Processing triggers for systemd (256.5-2ubuntu4) ...
 81s Processing triggers for man-db (2.12.1-3) ...
 82s Processing triggers for ca-certificates-java (20240118) ...
 82s Adding debian:ACCVRAIZ1.pem
 82s Adding debian:AC_RAIZ_FNMT-RCM.pem
 82s Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
 82s Adding debian:ANF_Secure_Server_Root_CA.pem
 82s Adding debian:Actalis_Authentication_Root_CA.pem
 82s Adding debian:AffirmTrust_Commercial.pem
 82s Adding debian:AffirmTrust_Networking.pem
 82s Adding debian:AffirmTrust_Premium.pem
 82s Adding debian:AffirmTrust_Premium_ECC.pem
 82s Adding debian:Amazon_Root_CA_1.pem
 82s Adding debian:Amazon_Root_CA_2.pem
 82s Adding debian:Amazon_Root_CA_3.pem
 82s Adding debian:Amazon_Root_CA_4.pem
 82s Adding debian:Atos_TrustedRoot_2011.pem
 82s Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
 82s Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
 82s Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
 82s Adding debian:BJCA_Global_Root_CA1.pem
 82s Adding debian:BJCA_Global_Root_CA2.pem
 82s Adding debian:Baltimore_CyberTrust_Root.pem
 82s Adding debian:Buypass_Class_2_Root_CA.pem
 82s Adding debian:Buypass_Class_3_Root_CA.pem
 82s Adding debian:CA_Disig_Root_R2.pem
 82s Adding debian:CFCA_EV_ROOT.pem
 82s Adding debian:COMODO_Certification_Authority.pem
 82s Adding debian:COMODO_ECC_Certification_Authority.pem
 82s Adding debian:COMODO_RSA_Certification_Authority.pem
 82s Adding debian:Certainly_Root_E1.pem
 82s Adding debian:Certainly_Root_R1.pem
 82s Adding debian:Certigna.pem
 82s Adding debian:Certigna_Root_CA.pem
 82s Adding debian:Certum_EC-384_CA.pem
 82s Adding debian:Certum_Trusted_Network_CA.pem
 82s Adding debian:Certum_Trusted_Network_CA_2.pem
 82s Adding debian:Certum_Trusted_Root_CA.pem
 82s Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
 82s Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
 82s Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
 82s Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
 82s Adding debian:Comodo_AAA_Services_root.pem
 82s Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
 82s Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
 82s Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
 82s Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
 82s Adding debian:DigiCert_Assured_ID_Root_CA.pem
 82s Adding debian:DigiCert_Assured_ID_Root_G2.pem
 82s Adding debian:DigiCert_Assured_ID_Root_G3.pem
 82s Adding debian:DigiCert_Global_Root_CA.pem
 82s Adding debian:DigiCert_Global_Root_G2.pem
 82s Adding debian:DigiCert_Global_Root_G3.pem
 82s Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
 82s Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
 82s Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
 82s Adding debian:DigiCert_Trusted_Root_G4.pem
 82s Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
 82s Adding debian:Entrust_Root_Certification_Authority.pem
 82s Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
 82s Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
 83s Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
 83s Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
 83s Adding debian:GLOBALTRUST_2020.pem
 83s Adding debian:GTS_Root_R1.pem
 83s Adding debian:GTS_Root_R2.pem
 83s Adding debian:GTS_Root_R3.pem
 83s Adding debian:GTS_Root_R4.pem
 83s Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
 83s Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
 83s Adding debian:GlobalSign_Root_CA.pem
 83s Adding debian:GlobalSign_Root_CA_-_R3.pem
 83s Adding debian:GlobalSign_Root_CA_-_R6.pem
 83s Adding debian:GlobalSign_Root_E46.pem
 83s Adding debian:GlobalSign_Root_R46.pem
 83s Adding debian:Go_Daddy_Class_2_CA.pem
 83s Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
 83s Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
 83s Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
 83s Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
 83s Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
 83s Adding debian:HiPKI_Root_CA_-_G1.pem
 83s Adding debian:Hongkong_Post_Root_CA_3.pem
 83s Adding debian:ISRG_Root_X1.pem
 83s Adding debian:ISRG_Root_X2.pem
 83s Adding debian:IdenTrust_Commercial_Root_CA_1.pem
 83s Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
 83s Adding debian:Izenpe.com.pem
 83s Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
 83s Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
 83s Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
 83s Adding debian:NAVER_Global_Root_Certification_Authority.pem
 83s Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
 83s Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
 83s Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
 83s Adding debian:QuoVadis_Root_CA_1_G3.pem
 83s Adding debian:QuoVadis_Root_CA_2.pem
 83s Adding debian:QuoVadis_Root_CA_2_G3.pem
 83s Adding debian:QuoVadis_Root_CA_3.pem
 83s Adding debian:QuoVadis_Root_CA_3_G3.pem
 83s Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
 83s Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
 83s Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
 83s Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
 83s Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
 83s Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
 83s Adding debian:SZAFIR_ROOT_CA2.pem
 83s Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
 83s Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
 83s Adding debian:SecureSign_RootCA11.pem
 83s Adding debian:SecureTrust_CA.pem
 83s Adding debian:Secure_Global_CA.pem
 83s Adding debian:Security_Communication_ECC_RootCA1.pem
 83s Adding debian:Security_Communication_RootCA2.pem
 83s Adding debian:Security_Communication_RootCA3.pem
 83s Adding debian:Security_Communication_Root_CA.pem
 83s Adding debian:Starfield_Class_2_CA.pem
 83s Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
 83s Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
 83s Adding debian:SwissSign_Gold_CA_-_G2.pem
 83s Adding debian:SwissSign_Silver_CA_-_G2.pem
 83s Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
 83s Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
 83s Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
 83s Adding debian:TWCA_Global_Root_CA.pem
 83s Adding debian:TWCA_Root_Certification_Authority.pem
 83s Adding debian:TeliaSonera_Root_CA_v1.pem
 83s Adding debian:Telia_Root_CA_v2.pem
 83s Adding debian:TrustAsia_Global_Root_CA_G3.pem
 83s Adding debian:TrustAsia_Global_Root_CA_G4.pem
 83s Adding debian:Trustwave_Global_Certification_Authority.pem
 83s Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
 83s Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
 83s Adding debian:TunTrust_Root_CA.pem
 83s Adding debian:UCA_Extended_Validation_Root.pem
 83s Adding debian:UCA_Global_G2_Root.pem
 83s Adding debian:USERTrust_ECC_Certification_Authority.pem
 83s Adding debian:USERTrust_RSA_Certification_Authority.pem
 83s Adding debian:XRamp_Global_CA_Root.pem
 83s Adding debian:certSIGN_ROOT_CA.pem
 83s Adding debian:certSIGN_Root_CA_G2.pem
 83s Adding debian:e-Szigno_Root_CA_2017.pem
 83s Adding debian:ePKI_Root_Certification_Authority.pem
 83s Adding debian:emSign_ECC_Root_CA_-_C3.pem
 83s Adding debian:emSign_ECC_Root_CA_-_G3.pem
 83s Adding debian:emSign_Root_CA_-_C1.pem
 83s Adding debian:emSign_Root_CA_-_G1.pem
 83s Adding debian:vTrus_ECC_Root_CA.pem
 83s Adding debian:vTrus_Root_CA.pem
 83s done.
 83s Setting up default-jre-headless (2:1.21-76) ...
 83s Setting up jaligner (1.0+dfsg-11) ...
 83s Setting up mhap (2.1.3+dfsg-3) ...
 83s Setting up canu (2.2+dfsg-5) ...
 83s Setting up circlator (1.5.6-11) ...
 83s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
 83s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
 83s /usr/lib/python3/dist-packages/circlator/dnaa.py:18: SyntaxWarning: invalid escape sequence '\s'
 83s   self.uniprot_search = re.sub('\s+', '+', uniprot_search.strip())
 83s Setting up autopkgtest-satdep (0) ...
 86s (Reading database ... 79393 files and directories currently installed.)
 86s Removing autopkgtest-satdep (0) ...
 87s autopkgtest [08:12:45]: test run-unit-test: [-----------------------
 87s + pkg=circlator
 87s + export LC_ALL=C.UTF-8
 87s + LC_ALL=C.UTF-8
 87s + '[' /tmp/autopkgtest.CKTTLW/autopkgtest_tmp = '' ']'
 87s + 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.CKTTLW/autopkgtest_tmp
 87s + cd /tmp/autopkgtest.CKTTLW/autopkgtest_tmp
 87s + tar xaf data.tar.xz
 87s + 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
 87s ++ py3versions --supported
 87s + for py in $(py3versions --supported 2> /dev/null)
 87s + eval dpkg-architecture --is amd64
 87s ++ dpkg-architecture --is amd64
 87s dpkg-architecture: warning: cannot determine CC system type, falling back to default (native compilation)
 87s + python3.13 -m pytest -v
 87s ============================= test session starts ==============================
 87s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13
 87s cachedir: .pytest_cache
 87s rootdir: /tmp/autopkgtest.CKTTLW/autopkgtest_tmp
 87s plugins: typeguard-4.4.1
 88s collecting ... collected 0 items / 11 errors
 88s 
 88s ==================================== ERRORS ====================================
 88s ______________________ ERROR collecting assemble_test.py _______________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/assemble_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s assemble_test.py:6: in <module>
 88s     from circlator import assemble
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ______________________ ERROR collecting assembly_test.py _______________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/assembly_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s assembly_test.py:7: in <module>
 88s     from circlator import assembly
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ______________________ ERROR collecting bamfilter_test.py ______________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/bamfilter_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s bamfilter_test.py:5: in <module>
 88s     from circlator import bamfilter
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ________________________ ERROR collecting clean_test.py ________________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/clean_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s clean_test.py:5: in <module>
 88s     from circlator import clean
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s _______________________ ERROR collecting common_test.py ________________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/common_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s common_test.py:3: in <module>
 88s     from circlator import common
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ________________________ ERROR collecting dnaa_test.py _________________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/dnaa_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s dnaa_test.py:5: in <module>
 88s     from circlator import dnaa
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ___________________ ERROR collecting external_progs_test.py ____________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/external_progs_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s external_progs_test.py:2: in <module>
 88s     from circlator import external_progs
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s _______________________ ERROR collecting mapping_test.py _______________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/mapping_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s mapping_test.py:5: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ________________________ ERROR collecting merge_test.py ________________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/merge_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s merge_test.py:8: in <module>
 88s     from circlator import merge
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s ______________________ ERROR collecting minimus2_test.py _______________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/minimus2_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s minimus2_test.py:6: in <module>
 88s     from circlator import minimus2
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s _____________________ ERROR collecting start_fixer_test.py _____________________
 88s ImportError while importing test module '/tmp/autopkgtest.CKTTLW/autopkgtest_tmp/start_fixer_test.py'.
 88s Hint: make sure your test modules/packages have valid Python names.
 88s Traceback:
 88s /usr/lib/python3.13/importlib/__init__.py:88: in import_module
 88s     return _bootstrap._gcd_import(name[level:], package, level)
 88s start_fixer_test.py:9: in <module>
 88s     from circlator import start_fixer
 88s /usr/lib/python3/dist-packages/circlator/__init__.py:26: in <module>
 88s     from circlator import *
 88s /usr/lib/python3/dist-packages/circlator/bamfilter.py:2: in <module>
 88s     import pysam
 88s /usr/lib/python3/dist-packages/pysam/__init__.py:4: in <module>
 88s     from pysam.libchtslib import *
 88s E   ModuleNotFoundError: No module named 'pysam.libchtslib'
 88s =============================== warnings summary ===============================
 88s ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
 88s   /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'}
 88s     __version__ = Distribution().from_name('pyfastaq').version
 88s 
 88s ../../../usr/lib/python3/dist-packages/circlator/__init__.py:1
 88s   /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
 88s     from pkg_resources import get_distribution
 88s 
 88s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
 88s =========================== short test summary info ============================
 88s ERROR assemble_test.py
 88s ERROR assembly_test.py
 88s ERROR bamfilter_test.py
 88s ERROR clean_test.py
 88s ERROR common_test.py
 88s ERROR dnaa_test.py
 88s ERROR external_progs_test.py
 88s ERROR mapping_test.py
 88s ERROR merge_test.py
 88s ERROR minimus2_test.py
 88s ERROR start_fixer_test.py
 88s !!!!!!!!!!!!!!!!!!! Interrupted: 11 errors during collection !!!!!!!!!!!!!!!!!!!
 88s ======================== 2 warnings, 11 errors in 0.34s ========================
 88s autopkgtest [08:12:46]: test run-unit-test: -----------------------]
 89s autopkgtest [08:12:47]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
 89s run-unit-test        FAIL non-zero exit status 2
 89s autopkgtest [08:12:47]: @@@@@@@@@@@@@@@@@@@@ summary
 89s run-unit-test        FAIL non-zero exit status 2
 95s nova [W] Skipping flock for amd64
 95s Creating nova instance adt-plucky-amd64-circlator-20241113-081118-juju-7f2275-prod-proposed-migration-environment-15-2b00bd27-8425-48c0-a1d0-63d3b2200bca from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...