0s autopkgtest [13:37:33]: starting date and time: 2024-11-14 13:37:33+0000
  0s autopkgtest [13:37:33]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:37:33]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.bqdvyk0h/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pyyaml --apt-upgrade idseq-bench --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pyyaml/6.0.2-1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-29.secgroup --name adt-plucky-arm64-idseq-bench-20241114-133732-juju-7f2275-prod-proposed-migration-environment-20-6f26f816-49f2-43be-9b82-9cd737f608fe --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/
102s autopkgtest [13:39:15]: testbed dpkg architecture: arm64
103s autopkgtest [13:39:16]: testbed apt version: 2.9.8
103s autopkgtest [13:39:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup
104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
104s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB]
104s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
104s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [983 kB]
104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [132 kB]
104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [715 kB]
104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6012 B]
105s Fetched 2088 kB in 1s (2061 kB/s)
105s Reading package lists...
107s Reading package lists...
108s Building dependency tree...
108s Reading state information...
109s Calculating upgrade...
109s The following packages will be upgraded:
109s   pastebinit python3-yaml
109s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
109s Need to get 179 kB of archives.
109s After this operation, 269 kB of additional disk space will be used.
109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-yaml arm64 6.0.2-1build1 [164 kB]
110s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB]
110s Fetched 179 kB in 0s (405 kB/s)
111s (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 ... 79925 files and directories currently installed.)
111s Preparing to unpack .../python3-yaml_6.0.2-1build1_arm64.deb ...
111s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ...
111s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ...
111s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
111s Setting up pastebinit (1.7.1-1) ...
111s Setting up python3-yaml (6.0.2-1build1) ...
111s Processing triggers for man-db (2.12.1-3) ...
112s Reading package lists...
112s Building dependency tree...
112s Reading state information...
113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
114s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
114s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
114s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
114s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
116s Reading package lists...
116s Reading package lists...
116s Building dependency tree...
116s Reading state information...
117s Calculating upgrade...
117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
121s autopkgtest [13:39:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
121s autopkgtest [13:39:34]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench
123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (dsc) [2356 B]
123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (tar) [17.3 kB]
123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (diff) [4432 B]
123s gpgv: Signature made Mon Jan 17 12:05:35 2022 UTC
123s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
123s gpgv:                issuer "nilesh@debian.org"
123s gpgv: Can't check signature: No public key
123s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-1.dsc: no acceptable signature found
123s autopkgtest [13:39:36]: testing package idseq-bench version 0.0~git20210602.27fb6dc-1
124s autopkgtest [13:39:37]: build not needed
124s autopkgtest [13:39:37]: test run-unit-test: preparing testbed
126s Reading package lists...
126s Building dependency tree...
126s Reading state information...
126s Starting pkgProblemResolver with broken count: 0
127s Starting 2 pkgProblemResolver with broken count: 0
127s Done
127s The following additional packages will be installed:
127s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35
127s   idseq-bench insilicoseq libblas3 libcairo2 libdeflate0 libfontconfig1
127s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64
127s   libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
127s   liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0
127s   libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0
127s   libxcb-shm0 libxrender1 ncbi-acc-download python3-all python3-biopython
127s   python3-cairo python3-decorator python3-freetype python3-joblib
127s   python3-numpy python3-pil python3-pysam python3-reportlab python3-rlpycairo
127s   python3-scipy python3-sklearn python3-sklearn-lib python3-smart-open
127s   python3-threadpoolctl python3-wrapt sgml-base w3c-sgml-lib x11-common
127s   xfonts-encodings xfonts-utils xml-core
127s Suggested packages:
127s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
127s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
127s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
127s   python3-rdflib python3-psycopg2 raxml samtools t-coffee wise
127s   python-joblib-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
127s   python-pil-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc
127s   rl-accel rl-renderpm python-scipy-doc python3-dap python-sklearn-doc
127s   ipython3 python3-azure python3-azure-storage sgml-base-doc debhelper
127s Recommended packages:
127s   python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson
127s   python3-psutil python3-olefile fonts-dejavu-extra g++ | c++-compiler
127s   python3-matplotlib python3-boto3 python3-paramiko python3-zstandard
127s The following NEW packages will be installed:
127s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-mono
127s   fonts-urw-base35 idseq-bench insilicoseq libblas3 libcairo2 libdeflate0
127s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
127s   libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0
127s   libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4
127s   libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7
127s   libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1
127s   ncbi-acc-download python3-all python3-biopython python3-cairo
127s   python3-decorator python3-freetype python3-joblib python3-numpy python3-pil
128s   python3-pysam python3-reportlab python3-rlpycairo python3-scipy
128s   python3-sklearn python3-sklearn-lib python3-smart-open python3-threadpoolctl
128s   python3-wrapt sgml-base w3c-sgml-lib x11-common xfonts-encodings
128s   xfonts-utils xml-core
128s 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded.
128s Need to get 57.2 MB/57.2 MB of archives.
128s After this operation, 230 MB of additional disk space will be used.
128s Get:1 /tmp/autopkgtest.UyobPn/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [764 B]
128s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB]
128s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
128s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
128s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB]
128s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
128s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
128s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB]
128s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
128s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB]
128s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
129s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
129s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
129s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
129s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB]
129s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB]
129s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB]
129s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
129s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB]
129s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB]
129s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
129s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB]
129s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB]
129s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB]
129s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
129s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB]
129s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB]
129s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB]
129s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
129s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB]
129s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB]
129s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB]
129s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB]
129s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
129s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
129s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
129s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
129s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
129s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB]
129s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB]
129s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
129s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB]
129s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB]
129s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
129s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB]
129s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB]
129s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB]
129s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB]
129s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
129s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
129s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB]
130s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 insilicoseq all 2.0.1-1 [4247 kB]
130s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-acc-download all 0.2.8-3 [13.3 kB]
130s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB]
130s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
130s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB]
130s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
130s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-wrapt arm64 1.15.0-3 [34.0 kB]
130s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-smart-open all 7.0.5-1 [89.9 kB]
130s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 idseq-bench all 0.0~git20210602.27fb6dc-1 [24.7 kB]
130s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B]
130s Fetched 57.2 MB in 2s (24.6 MB/s)
130s Selecting previously unselected package sgml-base.
130s (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 ... 79926 files and directories currently installed.)
130s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
130s Unpacking sgml-base (1.31) ...
131s Selecting previously unselected package fonts-dejavu-mono.
131s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
131s Unpacking fonts-dejavu-mono (2.37-8) ...
131s Selecting previously unselected package fonts-dejavu-core.
131s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
131s Unpacking fonts-dejavu-core (2.37-8) ...
131s Selecting previously unselected package libfontenc1:arm64.
131s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_arm64.deb ...
131s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ...
131s Selecting previously unselected package x11-common.
131s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ...
131s Unpacking x11-common (1:7.7+23ubuntu3) ...
131s Selecting previously unselected package xfonts-encodings.
131s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
131s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
131s Selecting previously unselected package xfonts-utils.
131s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_arm64.deb ...
131s Unpacking xfonts-utils (1:7.7+7) ...
131s Selecting previously unselected package fonts-urw-base35.
131s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ...
131s Unpacking fonts-urw-base35 (20200910-8) ...
131s Selecting previously unselected package fontconfig-config.
131s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ...
131s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
131s Selecting previously unselected package libblas3:arm64.
131s Preparing to unpack .../09-libblas3_3.12.0-3build2_arm64.deb ...
131s Unpacking libblas3:arm64 (3.12.0-3build2) ...
131s Selecting previously unselected package libgfortran5:arm64.
131s Preparing to unpack .../10-libgfortran5_14.2.0-8ubuntu1_arm64.deb ...
131s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ...
131s Selecting previously unselected package liblapack3:arm64.
132s Preparing to unpack .../11-liblapack3_3.12.0-3build2_arm64.deb ...
132s Unpacking liblapack3:arm64 (3.12.0-3build2) ...
132s Selecting previously unselected package python3-numpy.
132s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ...
132s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
132s Selecting previously unselected package libgomp1:arm64.
132s Preparing to unpack .../13-libgomp1_14.2.0-8ubuntu1_arm64.deb ...
132s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ...
132s Selecting previously unselected package libimagequant0:arm64.
132s Preparing to unpack .../14-libimagequant0_2.18.0-1build1_arm64.deb ...
132s Unpacking libimagequant0:arm64 (2.18.0-1build1) ...
132s Selecting previously unselected package libjpeg-turbo8:arm64.
132s Preparing to unpack .../15-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ...
132s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
132s Selecting previously unselected package libjpeg8:arm64.
132s Preparing to unpack .../16-libjpeg8_8c-2ubuntu11_arm64.deb ...
132s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
132s Selecting previously unselected package liblcms2-2:arm64.
132s Preparing to unpack .../17-liblcms2-2_2.16-2_arm64.deb ...
132s Unpacking liblcms2-2:arm64 (2.16-2) ...
132s Selecting previously unselected package libopenjp2-7:arm64.
132s Preparing to unpack .../18-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ...
132s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
132s Selecting previously unselected package libgraphite2-3:arm64.
132s Preparing to unpack .../19-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
132s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
132s Selecting previously unselected package libharfbuzz0b:arm64.
132s Preparing to unpack .../20-libharfbuzz0b_10.0.1-1_arm64.deb ...
132s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ...
132s Selecting previously unselected package libraqm0:arm64.
132s Preparing to unpack .../21-libraqm0_0.10.1-1build1_arm64.deb ...
132s Unpacking libraqm0:arm64 (0.10.1-1build1) ...
132s Selecting previously unselected package libdeflate0:arm64.
132s Preparing to unpack .../22-libdeflate0_1.22-1_arm64.deb ...
132s Unpacking libdeflate0:arm64 (1.22-1) ...
132s Selecting previously unselected package libjbig0:arm64.
132s Preparing to unpack .../23-libjbig0_2.1-6.1ubuntu2_arm64.deb ...
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133s Selecting previously unselected package libwebpdemux2:arm64.
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135s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ...
135s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ...
135s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
135s Setting up python3-joblib (1.3.2-5) ...
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136s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ...
136s Setting up python3-freetype (2.5.1-1) ...
137s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
137s Setting up python3-decorator (5.1.1-5) ...
137s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ...
137s Setting up libblas3:arm64 (3.12.0-3build2) ...
137s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
137s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
137s Setting up libimagequant0:arm64 (2.18.0-1build1) ...
137s Setting up fonts-dejavu-mono (2.37-8) ...
137s Setting up python3-wrapt (1.15.0-3) ...
137s Setting up fonts-dejavu-core (2.37-8) ...
137s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ...
137s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
137s Setting up libwebp7:arm64 (1.4.0-0.1) ...
137s Setting up libhts3t64:arm64 (1.20+ds-1) ...
137s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ...
137s Setting up ncbi-acc-download (0.2.8-3) ...
137s Setting up libharfbuzz0b:arm64 (10.0.1-1) ...
137s Setting up sgml-base (1.31) ...
137s Setting up libwebpmux3:arm64 (1.4.0-0.1) ...
137s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
137s Setting up liblapack3:arm64 (3.12.0-3build2) ...
137s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
137s Setting up python3-pysam (0.22.1+ds-2) ...
137s Setting up python3-smart-open (7.0.5-1) ...
138s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
138s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ...
138s Setting up xfonts-utils (1:7.7+7) ...
138s Setting up libraqm0:arm64 (0.10.1-1build1) ...
138s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
140s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
140s Setting up xml-core (0.19) ...
140s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ...
140s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
140s Setting up python3-scipy (1.13.1-5) ...
145s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ...
145s Setting up fonts-urw-base35 (20200910-8) ...
145s Setting up libcairo2:arm64 (1.18.2-2) ...
145s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ...
145s Setting up python3-sklearn (1.4.2+dfsg-6) ...
147s Setting up python3-cairo (1.26.1-2) ...
148s Setting up python3-rlpycairo (0.3.0-3) ...
148s Setting up python3-reportlab (4.2.5-1) ...
149s Processing triggers for libc-bin (2.40-1ubuntu3) ...
149s Processing triggers for man-db (2.12.1-3) ...
150s Processing triggers for sgml-base (1.31) ...
150s Setting up w3c-sgml-lib (1.3-3) ...
179s Setting up python3-biopython (1.84+dfsg-4) ...
180s Setting up insilicoseq (2.0.1-1) ...
180s Setting up idseq-bench (0.0~git20210602.27fb6dc-1) ...
180s Setting up autopkgtest-satdep (0) ...
184s (Reading database ... 86245 files and directories currently installed.)
184s Removing autopkgtest-satdep (0) ...
185s autopkgtest [13:40:38]: test run-unit-test: [-----------------------
432s INFO:iss.app:Starting iss generate
432s INFO:iss.generator:Using kde ErrorModel
432s INFO:iss.util:Stitching input files together
433s INFO:iss.generator:Using abundance file:norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4519_abundance.txt
433s INFO:iss.app:Using 2 cpus for read generation
433s INFO:iss.app:Generating 60000 reads
464s INFO:iss.util:Stitching input files together
464s INFO:iss.util:Stitching input files together
464s INFO:iss.util:Cleaning up
464s INFO:iss.app:Read generation complete
473s Generating IDseq benchmark data...
473s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all'
473s 'cat downloads/NC_016845.1.fa > downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta'
473s "grep -v '^>' downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta | tr -d '\n' | wc > bateria__klebsiella_pneumoniae_HS11286__1125630.size"
473s Genome bateria__klebsiella_pneumoniae_HS11286__1125630 size 5333942 bases.
473s 'cd downloads; ncbi-acc-download --format fasta NC_007194.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007195.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007196.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007197.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007198.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007199.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007200.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_007201.1 -e all'
473s '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'
473s "grep -v '^>' downloads/fungi__aspergillus_fumigatus__330879.fasta | tr -d '\n' | wc > fungi__aspergillus_fumigatus__330879.size"
473s Genome fungi__aspergillus_fumigatus__330879 size 29384958 bases.
473s 'cd downloads; ncbi-acc-download --format fasta MG148341.1 -e all'
473s 'cat downloads/MG148341.1.fa > downloads/viruses__rhinovirus_c__463676.fasta'
473s "grep -v '^>' downloads/viruses__rhinovirus_c__463676.fasta | tr -d '\n' | wc > viruses__rhinovirus_c__463676.size"
473s Genome viruses__rhinovirus_c__463676 size 7056 bases.
473s 'cd downloads; ncbi-acc-download --format fasta MG049915.1 -e all'
473s 'cat downloads/MG049915.1.fa > downloads/viruses__chikungunya__37124.fasta'
473s "grep -v '^>' downloads/viruses__chikungunya__37124.fasta | tr -d '\n' | wc > viruses__chikungunya__37124.size"
473s Genome viruses__chikungunya__37124 size 11604 bases.
473s 'cd downloads; ncbi-acc-download --format fasta NC_007795.1 -e all'
473s 'cat downloads/NC_007795.1.fa > downloads/bateria__staphylococcus_aureus__93061.fasta'
473s "grep -v '^>' downloads/bateria__staphylococcus_aureus__93061.fasta | tr -d '\n' | wc > bateria__staphylococcus_aureus__93061.size"
473s Genome bateria__staphylococcus_aureus__93061 size 2821361 bases.
473s 'cd downloads; ncbi-acc-download --format fasta NC_004325.2 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_037280.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_000521.4 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004318.2 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004326.2 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004327.3 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004328.3 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004329.3 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004330.2 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_037281.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_037282.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_037284.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_004331.3 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_037283.1 -e all'
473s 'cd downloads; ncbi-acc-download --format fasta NC_036769.1 -e all'
473s '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'
473s "grep -v '^>' downloads/protista__plasmodium_falciuparum__36329.fasta | tr -d '\n' | wc > protista__plasmodium_falciuparum__36329.size"
473s Genome protista__plasmodium_falciuparum__36329 size 23326872 bases.
473s Initializing and downloading genomes...
473s GENERATING norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6
473s 'iss --version > iss_version.txt'
473s '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_4519_genomes.fasta'
473s 'iss generate --n_reads 60000 --genomes norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4519_genomes.fasta --model hiseq --abundance_file norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4519_abundance.txt --gc_bias --output norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_4519 --cpus 2'
473s *** 100.0 percent done, 0.7 minutes elapsed, 0.0 minutes remaining, ETA 13:45:26 ***
473s 
473s autopkgtest [13:45:26]: test run-unit-test: -----------------------]
474s autopkgtest [13:45:27]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
474s run-unit-test        PASS
474s autopkgtest [13:45:27]: @@@@@@@@@@@@@@@@@@@@ summary
474s run-unit-test        PASS
486s nova [W] Skipping flock in bos03-arm64
486s Creating nova instance adt-plucky-arm64-idseq-bench-20241114-133732-juju-7f2275-prod-proposed-migration-environment-20-6f26f816-49f2-43be-9b82-9cd737f608fe from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...