0s autopkgtest [13:31:30]: starting date and time: 2024-11-13 13:31:30+0000
  0s autopkgtest [13:31:30]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:31:30]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x1vqz6ox/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 idseq-bench --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-14.secgroup --name adt-plucky-ppc64el-idseq-bench-20241113-133130-juju-7f2275-prod-proposed-migration-environment-20-b4da9b16-11ac-4bb5-b003-35872b62e53f --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
116s autopkgtest [13:33:26]: testbed dpkg architecture: ppc64el
116s autopkgtest [13:33:26]: testbed apt version: 2.9.8
116s autopkgtest [13:33:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup
117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
117s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB]
117s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
117s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB]
118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
118s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [107 kB]
118s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [668 kB]
118s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.4 kB]
118s Fetched 1963 kB in 1s (1917 kB/s)
118s Reading package lists...
120s Reading package lists...
121s Building dependency tree...
121s Reading state information...
121s Calculating upgrade...
121s The following NEW packages will be installed:
121s   python3.13-gdbm
121s The following packages will be upgraded:
121s   libpython3-stdlib python3 python3-gdbm python3-minimal
121s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
121s Need to get 102 kB of archives.
121s After this operation, 141 kB of additional disk space will be used.
121s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
121s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
121s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
121s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
121s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
122s Fetched 102 kB in 0s (271 kB/s)
122s (Reading database ... 
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
122s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
122s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
122s Setting up python3-minimal (3.12.7-1) ...
122s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
122s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ...
122s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
122s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ...
122s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ...
122s Selecting previously unselected package python3.13-gdbm.
122s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ...
122s Unpacking python3.13-gdbm (3.13.0-2) ...
122s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ...
122s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
122s Setting up python3.13-gdbm (3.13.0-2) ...
122s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
122s Setting up python3 (3.12.7-1) ...
122s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
122s Processing triggers for man-db (2.12.1-3) ...
123s Reading package lists...
123s Building dependency tree...
123s Reading state information...
124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
124s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
124s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
124s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
125s Reading package lists...
125s Reading package lists...
126s Building dependency tree...
126s Reading state information...
126s Calculating upgrade...
126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
126s Reading package lists...
126s Building dependency tree...
126s Reading state information...
126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
129s autopkgtest [13:33:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
129s autopkgtest [13:33:39]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench
131s Get:1 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (dsc) [2356 B]
131s Get:2 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (tar) [17.3 kB]
131s Get:3 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (diff) [4432 B]
131s gpgv: Signature made Mon Jan 17 12:05:35 2022 UTC
131s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
131s gpgv:                issuer "nilesh@debian.org"
131s gpgv: Can't check signature: No public key
131s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-1.dsc: no acceptable signature found
131s autopkgtest [13:33:41]: testing package idseq-bench version 0.0~git20210602.27fb6dc-1
131s autopkgtest [13:33:41]: build not needed
132s autopkgtest [13:33:42]: test run-unit-test: preparing testbed
133s Reading package lists...
133s Building dependency tree...
133s Reading state information...
133s Starting pkgProblemResolver with broken count: 0
133s Starting 2 pkgProblemResolver with broken count: 0
133s Done
134s The following additional packages will be installed:
134s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35
134s   idseq-bench insilicoseq libblas3 libcairo2 libdeflate0 libfontconfig1
134s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64
134s   libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
134s   liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0
134s   libpython3.13-minimal libpython3.13-stdlib libraqm0 libsharpyuv0 libtiff6
134s   libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1
134s   ncbi-acc-download python3-all python3-biopython python3-cairo
134s   python3-decorator python3-freetype python3-joblib python3-numpy python3-pil
134s   python3-pysam python3-reportlab python3-rlpycairo python3-scipy
134s   python3-sklearn python3-sklearn-lib python3-smart-open python3-threadpoolctl
134s   python3-wrapt python3.13 python3.13-minimal sgml-base w3c-sgml-lib
134s   x11-common xfonts-encodings xfonts-utils xml-core
134s Suggested packages:
134s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
134s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
134s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
134s   python3-rdflib python3-psycopg2 raxml samtools t-coffee wise
134s   python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
134s   python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
134s   rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc
134s   ipython3 python3-azure python3-azure-storage python3.13-venv python3.13-doc
134s   binfmt-support sgml-base-doc debhelper
134s Recommended packages:
134s   python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson
134s   python3-psutil python3-olefile fonts-dejavu-extra g++ | c++-compiler
134s   python3-matplotlib python3-boto3 python3-paramiko python3-zstandard
134s The following NEW packages will be installed:
134s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono
134s   fonts-urw-base35 idseq-bench insilicoseq libblas3 libcairo2 libdeflate0
134s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
134s   libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0
134s   libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4
134s   libopenjp2-7 libpixman-1-0 libpython3.13-minimal libpython3.13-stdlib
134s   libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3
134s   libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download python3-all
134s   python3-biopython python3-cairo python3-decorator python3-freetype
134s   python3-joblib python3-numpy python3-pil python3-pysam python3-reportlab
134s   python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib
134s   python3-smart-open python3-threadpoolctl python3-wrapt python3.13
134s   python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings
134s   xfonts-utils xml-core
134s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded.
134s Need to get 68.7 MB/68.7 MB of archives.
134s After this operation, 287 MB of additional disk space will be used.
134s Get:1 /tmp/autopkgtest.4vjsMA/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [764 B]
134s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB]
134s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB]
134s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB]
134s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
134s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
134s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB]
134s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB]
134s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
134s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB]
134s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB]
135s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
135s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
135s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
135s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
135s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
135s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB]
135s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB]
135s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB]
135s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
135s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB]
135s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB]
135s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
135s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB]
135s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB]
135s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB]
135s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
135s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB]
135s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB]
135s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB]
135s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
135s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB]
135s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB]
135s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB]
135s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
135s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
135s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
135s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
135s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
135s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
135s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB]
135s Get:42 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB]
135s Get:43 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B]
135s Get:44 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB]
135s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB]
135s Get:46 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB]
135s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB]
135s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB]
135s Get:49 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB]
135s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB]
135s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
135s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB]
135s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB]
136s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el insilicoseq all 2.0.1-1 [4247 kB]
136s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ncbi-acc-download all 0.2.8-3 [13.3 kB]
136s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB]
136s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB]
136s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB]
136s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
136s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-wrapt ppc64el 1.15.0-3 [35.6 kB]
136s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-smart-open all 7.0.5-1 [89.9 kB]
136s Get:62 http://ftpmaster.internal/ubuntu plucky/universe ppc64el idseq-bench all 0.0~git20210602.27fb6dc-1 [24.7 kB]
136s Get:63 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB]
136s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB]
136s Get:65 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B]
137s Fetched 68.7 MB in 3s (25.1 MB/s)
137s Selecting previously unselected package libpython3.13-minimal:ppc64el.
137s (Reading database ... 
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73774 files and directories currently installed.)
137s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ...
137s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ...
137s Selecting previously unselected package python3.13-minimal.
137s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ...
137s Unpacking python3.13-minimal (3.13.0-2) ...
137s Selecting previously unselected package sgml-base.
137s Preparing to unpack .../02-sgml-base_1.31_all.deb ...
137s Unpacking sgml-base (1.31) ...
137s Selecting previously unselected package fonts-dejavu-mono.
137s Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ...
137s Unpacking fonts-dejavu-mono (2.37-8) ...
137s Selecting previously unselected package fonts-dejavu-core.
137s Preparing to unpack .../04-fonts-dejavu-core_2.37-8_all.deb ...
137s Unpacking fonts-dejavu-core (2.37-8) ...
137s Selecting previously unselected package libfontenc1:ppc64el.
137s Preparing to unpack .../05-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ...
137s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ...
137s Selecting previously unselected package x11-common.
137s Preparing to unpack .../06-x11-common_1%3a7.7+23ubuntu3_all.deb ...
137s Unpacking x11-common (1:7.7+23ubuntu3) ...
137s Selecting previously unselected package xfonts-encodings.
137s Preparing to unpack .../07-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
137s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
137s Selecting previously unselected package xfonts-utils.
137s Preparing to unpack .../08-xfonts-utils_1%3a7.7+7_ppc64el.deb ...
137s Unpacking xfonts-utils (1:7.7+7) ...
137s Selecting previously unselected package fonts-urw-base35.
137s Preparing to unpack .../09-fonts-urw-base35_20200910-8_all.deb ...
137s Unpacking fonts-urw-base35 (20200910-8) ...
137s Selecting previously unselected package fontconfig-config.
137s Preparing to unpack .../10-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ...
137s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
137s Selecting previously unselected package libblas3:ppc64el.
137s Preparing to unpack .../11-libblas3_3.12.0-3build2_ppc64el.deb ...
137s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
137s Selecting previously unselected package libgfortran5:ppc64el.
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137s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
137s Selecting previously unselected package liblapack3:ppc64el.
137s Preparing to unpack .../13-liblapack3_3.12.0-3build2_ppc64el.deb ...
137s Unpacking liblapack3:ppc64el (3.12.0-3build2) ...
137s Selecting previously unselected package python3-numpy.
137s Preparing to unpack .../14-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ...
137s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
138s Selecting previously unselected package libgomp1:ppc64el.
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138s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ...
138s Selecting previously unselected package libimagequant0:ppc64el.
138s Preparing to unpack .../16-libimagequant0_2.18.0-1build1_ppc64el.deb ...
138s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ...
138s Selecting previously unselected package libjpeg-turbo8:ppc64el.
138s Preparing to unpack .../17-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ...
138s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ...
138s Selecting previously unselected package libjpeg8:ppc64el.
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138s Selecting previously unselected package liblcms2-2:ppc64el.
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138s Selecting previously unselected package libopenjp2-7:ppc64el.
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138s Selecting previously unselected package libgraphite2-3:ppc64el.
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138s Selecting previously unselected package libharfbuzz0b:ppc64el.
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138s Selecting previously unselected package libraqm0:ppc64el.
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138s Selecting previously unselected package libdeflate0:ppc64el.
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138s Unpacking libdeflate0:ppc64el (1.22-1) ...
138s Selecting previously unselected package libjbig0:ppc64el.
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138s Selecting previously unselected package libsharpyuv0:ppc64el.
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138s Selecting previously unselected package libwebp7:ppc64el.
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138s Selecting previously unselected package libtiff6:ppc64el.
138s Preparing to unpack .../29-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ...
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138s Selecting previously unselected package libwebpdemux2:ppc64el.
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138s Selecting previously unselected package libwebpmux3:ppc64el.
138s Preparing to unpack .../31-libwebpmux3_1.4.0-0.1_ppc64el.deb ...
138s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ...
138s Selecting previously unselected package python3-pil:ppc64el.
138s Preparing to unpack .../32-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ...
138s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ...
138s Selecting previously unselected package libfontconfig1:ppc64el.
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138s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
138s Selecting previously unselected package libpixman-1-0:ppc64el.
138s Preparing to unpack .../34-libpixman-1-0_0.44.0-3_ppc64el.deb ...
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138s Selecting previously unselected package libxcb-render0:ppc64el.
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138s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ...
138s Selecting previously unselected package libxrender1:ppc64el.
138s Preparing to unpack .../37-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ...
138s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ...
138s Selecting previously unselected package libcairo2:ppc64el.
138s Preparing to unpack .../38-libcairo2_1.18.2-2_ppc64el.deb ...
138s Unpacking libcairo2:ppc64el (1.18.2-2) ...
138s Selecting previously unselected package python3-cairo.
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138s Unpacking python3-cairo (1.26.1-2) ...
138s Selecting previously unselected package python3-freetype.
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138s Selecting previously unselected package python3-rlpycairo.
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138s Selecting previously unselected package python3-reportlab.
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138s Selecting previously unselected package xml-core.
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138s Selecting previously unselected package w3c-sgml-lib.
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138s Selecting previously unselected package python3-biopython.
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138s Selecting previously unselected package libhtscodecs2:ppc64el.
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138s Selecting previously unselected package libhts3t64:ppc64el.
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139s Selecting previously unselected package python3-pysam.
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139s Selecting previously unselected package liblbfgsb0:ppc64el.
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139s Selecting previously unselected package ncbi-acc-download.
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139s Selecting previously unselected package python3-joblib.
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139s Selecting previously unselected package python3-sklearn-lib:ppc64el.
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140s Unpacking python3-smart-open (7.0.5-1) ...
140s Selecting previously unselected package idseq-bench.
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140s Unpacking idseq-bench (0.0~git20210602.27fb6dc-1) ...
140s Selecting previously unselected package libpython3.13-stdlib:ppc64el.
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140s Selecting previously unselected package python3.13.
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140s Unpacking python3.13 (3.13.0-2) ...
140s Selecting previously unselected package python3-all.
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140s Selecting previously unselected package autopkgtest-satdep.
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140s Unpacking autopkgtest-satdep (0) ...
140s Setting up libhtscodecs2:ppc64el (1.6.1-1) ...
140s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
140s Setting up liblcms2-2:ppc64el (2.16-2) ...
140s Setting up libpixman-1-0:ppc64el (0.44.0-3) ...
140s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ...
140s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ...
140s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ...
140s Setting up python3-joblib (1.3.2-5) ...
140s Setting up libxcb-render0:ppc64el (1.17.0-2) ...
140s Setting up python3-threadpoolctl (3.1.0-1) ...
141s Setting up x11-common (1:7.7+23ubuntu3) ...
141s Setting up libdeflate0:ppc64el (1.22-1) ...
141s Setting up libxcb-shm0:ppc64el (1.17.0-2) ...
141s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ...
141s Setting up python3-freetype (2.5.1-1) ...
141s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ...
141s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ...
141s Setting up python3-decorator (5.1.1-5) ...
141s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ...
141s Setting up libblas3:ppc64el (3.12.0-3build2) ...
141s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
141s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
141s Setting up libimagequant0:ppc64el (2.18.0-1build1) ...
141s Setting up fonts-dejavu-mono (2.37-8) ...
141s Setting up python3-wrapt (1.15.0-3) ...
142s Setting up fonts-dejavu-core (2.37-8) ...
142s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ...
142s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
142s Setting up libwebp7:ppc64el (1.4.0-0.1) ...
142s Setting up libhts3t64:ppc64el (1.20+ds-1) ...
142s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ...
142s Setting up python3.13-minimal (3.13.0-2) ...
143s Setting up ncbi-acc-download (0.2.8-3) ...
143s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ...
143s Setting up sgml-base (1.31) ...
143s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ...
143s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ...
143s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
143s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
143s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
143s Setting up python3-pysam (0.22.1+ds-2) ...
143s Setting up python3-smart-open (7.0.5-1) ...
143s Setting up python3.13 (3.13.0-2) ...
144s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
145s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ...
145s Setting up python3-all (3.12.7-1) ...
145s Setting up xfonts-utils (1:7.7+7) ...
145s Setting up libraqm0:ppc64el (0.10.1-1build1) ...
145s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
149s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
149s Setting up xml-core (0.19) ...
149s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
149s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
149s Setting up python3-scipy (1.13.1-5) ...
157s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ...
157s Setting up fonts-urw-base35 (20200910-8) ...
157s Setting up libcairo2:ppc64el (1.18.2-2) ...
157s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ...
158s Setting up python3-sklearn (1.4.2+dfsg-6) ...
162s Setting up python3-cairo (1.26.1-2) ...
163s Setting up python3-rlpycairo (0.3.0-3) ...
163s Setting up python3-reportlab (4.2.5-1) ...
164s Processing triggers for libc-bin (2.40-1ubuntu3) ...
164s Processing triggers for systemd (256.5-2ubuntu4) ...
164s Processing triggers for man-db (2.12.1-3) ...
166s Processing triggers for sgml-base (1.31) ...
166s Setting up w3c-sgml-lib (1.3-3) ...
200s Setting up python3-biopython (1.84+dfsg-4) ...
203s Setting up insilicoseq (2.0.1-1) ...
203s Setting up idseq-bench (0.0~git20210602.27fb6dc-1) ...
203s Setting up autopkgtest-satdep (0) ...
207s (Reading database ... 80827 files and directories currently installed.)
207s Removing autopkgtest-satdep (0) ...
208s autopkgtest [13:34:57]: test run-unit-test: [-----------------------
390s INFO:iss.app:Starting iss generate
390s INFO:iss.generator:Using kde ErrorModel
390s INFO:iss.util:Stitching input files together
390s INFO:iss.generator:Using abundance file:norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4840_abundance.txt
390s INFO:iss.app:Using 2 cpus for read generation
390s INFO:iss.app:Generating 60000 reads
440s INFO:iss.util:Stitching input files together
440s INFO:iss.util:Stitching input files together
440s INFO:iss.util:Cleaning up
440s INFO:iss.app:Read generation complete
450s Generating IDseq benchmark data...
450s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all'
450s 'cat downloads/NC_016845.1.fa > downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta'
450s "grep -v '^>' downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta | tr -d '\n' | wc > bateria__klebsiella_pneumoniae_HS11286__1125630.size"
450s Genome bateria__klebsiella_pneumoniae_HS11286__1125630 size 5333942 bases.
450s 'cd downloads; ncbi-acc-download --format fasta NC_007194.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007195.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007196.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007197.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007198.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007199.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007200.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_007201.1 -e all'
450s 'cat downloads/NC_007194.1.fa downloads/NC_007195.1.fa downloads/NC_007196.1.fa downloads/NC_007197.1.fa downloads/NC_007198.1.fa downloads/NC_007199.1.fa downloads/NC_007200.1.fa downloads/NC_007201.1.fa > downloads/fungi__aspergillus_fumigatus__330879.fasta'
450s "grep -v '^>' downloads/fungi__aspergillus_fumigatus__330879.fasta | tr -d '\n' | wc > fungi__aspergillus_fumigatus__330879.size"
450s Genome fungi__aspergillus_fumigatus__330879 size 29384958 bases.
450s 'cd downloads; ncbi-acc-download --format fasta MG148341.1 -e all'
450s 'cat downloads/MG148341.1.fa > downloads/viruses__rhinovirus_c__463676.fasta'
450s "grep -v '^>' downloads/viruses__rhinovirus_c__463676.fasta | tr -d '\n' | wc > viruses__rhinovirus_c__463676.size"
450s Genome viruses__rhinovirus_c__463676 size 7056 bases.
450s 'cd downloads; ncbi-acc-download --format fasta MG049915.1 -e all'
450s 'cat downloads/MG049915.1.fa > downloads/viruses__chikungunya__37124.fasta'
450s "grep -v '^>' downloads/viruses__chikungunya__37124.fasta | tr -d '\n' | wc > viruses__chikungunya__37124.size"
450s Genome viruses__chikungunya__37124 size 11604 bases.
450s 'cd downloads; ncbi-acc-download --format fasta NC_007795.1 -e all'
450s 'cat downloads/NC_007795.1.fa > downloads/bateria__staphylococcus_aureus__93061.fasta'
450s "grep -v '^>' downloads/bateria__staphylococcus_aureus__93061.fasta | tr -d '\n' | wc > bateria__staphylococcus_aureus__93061.size"
450s Genome bateria__staphylococcus_aureus__93061 size 2821361 bases.
450s 'cd downloads; ncbi-acc-download --format fasta NC_004325.2 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_037280.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_000521.4 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004318.2 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004326.2 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004327.3 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004328.3 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004329.3 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004330.2 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_037281.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_037282.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_037284.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_004331.3 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_037283.1 -e all'
450s 'cd downloads; ncbi-acc-download --format fasta NC_036769.1 -e all'
450s 'cat downloads/NC_004325.2.fa downloads/NC_037280.1.fa downloads/NC_000521.4.fa downloads/NC_004318.2.fa downloads/NC_004326.2.fa downloads/NC_004327.3.fa downloads/NC_004328.3.fa downloads/NC_004329.3.fa downloads/NC_004330.2.fa downloads/NC_037281.1.fa downloads/NC_037282.1.fa downloads/NC_037284.1.fa downloads/NC_004331.3.fa downloads/NC_037283.1.fa downloads/NC_036769.1.fa > downloads/protista__plasmodium_falciuparum__36329.fasta'
450s "grep -v '^>' downloads/protista__plasmodium_falciuparum__36329.fasta | tr -d '\n' | wc > protista__plasmodium_falciuparum__36329.size"
450s Genome protista__plasmodium_falciuparum__36329 size 23326872 bases.
450s Initializing and downloading genomes...
450s GENERATING norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6
450s 'iss --version > iss_version.txt'
450s 'cat downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta downloads/fungi__aspergillus_fumigatus__330879.fasta downloads/viruses__rhinovirus_c__463676.fasta downloads/viruses__chikungunya__37124.fasta downloads/bateria__staphylococcus_aureus__93061.fasta downloads/protista__plasmodium_falciuparum__36329.fasta > norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4840_genomes.fasta'
450s 'iss generate --n_reads 60000 --genomes norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4840_genomes.fasta --model hiseq --abundance_file norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4840_abundance.txt --gc_bias --output norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4840 --cpus 2'
450s *** 100.0 percent done, 1.0 minutes elapsed, 0.0 minutes remaining, ETA 13:39:00 ***
450s 
451s autopkgtest [13:39:01]: test run-unit-test: -----------------------]
451s run-unit-test        PASS
451s autopkgtest [13:39:01]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
452s autopkgtest [13:39:02]: @@@@@@@@@@@@@@@@@@@@ summary
452s run-unit-test        PASS
465s nova [W] Using flock in prodstack6-ppc64el
465s Creating nova instance adt-plucky-ppc64el-idseq-bench-20241113-133130-juju-7f2275-prod-proposed-migration-environment-20-b4da9b16-11ac-4bb5-b003-35872b62e53f from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...