0s autopkgtest [13:01:10]: starting date and time: 2024-11-14 13:01:10+0000
  0s autopkgtest [13:01:10]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:01:10]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vejwagkb/out --timeout-copy=6000 -a i386 --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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-12.secgroup --name adt-plucky-i386-idseq-bench-20241114-130110-juju-7f2275-prod-proposed-migration-environment-15-0a245cfe-9b22-437f-a992-c7cc330b9d81 --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/
 51s autopkgtest [13:02:01]: testbed dpkg architecture: amd64
 51s autopkgtest [13:02:01]: testbed apt version: 2.9.8
 52s autopkgtest [13:02:02]: test architecture: i386
 52s autopkgtest [13:02:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 53s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [983 kB]
 53s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 53s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB]
 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.9 kB]
 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [138 kB]
 53s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 53s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [749 kB]
 53s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [291 kB]
 53s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B]
 53s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B]
 53s Fetched 2484 kB in 1s (3067 kB/s)
 53s Reading package lists...
 56s Reading package lists...
 56s Building dependency tree...
 56s Reading state information...
 56s Calculating upgrade...
 56s The following NEW packages will be installed:
 56s   python3.13-gdbm
 56s The following packages will be upgraded:
 56s   libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal
 57s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 57s Need to get 116 kB of archives.
 57s After this operation, 100 kB of additional disk space will be used.
 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 57s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 57s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 57s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 57s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB]
 57s Fetched 116 kB in 1s (171 kB/s)
 58s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 15%
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(Reading database ... 25%
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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 ... 75542 files and directories currently installed.)
 58s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 58s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 58s Setting up python3-minimal (3.12.7-1) ...
 58s (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 ... 75542 files and directories currently installed.)
 58s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 58s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 58s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 58s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 58s Selecting previously unselected package python3.13-gdbm.
 58s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
 58s Unpacking python3.13-gdbm (3.13.0-2) ...
 58s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
 58s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 58s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ...
 58s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
 58s Setting up python3.13-gdbm (3.13.0-2) ...
 58s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 58s Setting up python3 (3.12.7-1) ...
 58s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 58s Setting up pastebinit (1.7.1-1) ...
 58s Processing triggers for man-db (2.12.1-3) ...
 59s Reading package lists...
 59s Building dependency tree...
 59s Reading state information...
 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 61s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 61s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 62s Reading package lists...
 62s Reading package lists...
 62s Building dependency tree...
 62s Reading state information...
 62s Calculating upgrade...
 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 62s Reading package lists...
 62s Building dependency tree...
 62s Reading state information...
 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 65s autopkgtest [13:02:15]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 65s autopkgtest [13:02:15]: @@@@@@@@@@@@@@@@@@@@ apt-source idseq-bench
 67s Get:1 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (dsc) [2356 B]
 67s Get:2 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (tar) [17.3 kB]
 67s Get:3 http://ftpmaster.internal/ubuntu plucky/universe idseq-bench 0.0~git20210602.27fb6dc-1 (diff) [4432 B]
 67s gpgv: Signature made Mon Jan 17 12:05:35 2022 UTC
 67s gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
 67s gpgv:                issuer "nilesh@debian.org"
 67s gpgv: Can't check signature: No public key
 67s dpkg-source: warning: cannot verify inline signature for ./idseq-bench_0.0~git20210602.27fb6dc-1.dsc: no acceptable signature found
 67s autopkgtest [13:02:17]: testing package idseq-bench version 0.0~git20210602.27fb6dc-1
 67s autopkgtest [13:02:17]: build not needed
 68s autopkgtest [13:02:18]: test run-unit-test: preparing testbed
 70s Note, using file '/tmp/autopkgtest.j1wxzW/1-autopkgtest-satdep.dsc' to get the build dependencies
 70s Reading package lists...
 70s Building dependency tree...
 70s Reading state information...
 71s Starting pkgProblemResolver with broken count: 0
 71s Starting 2 pkgProblemResolver with broken count: 0
 71s Done
 71s The following NEW packages will be installed:
 71s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
 71s   fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-urw-base35 g++
 71s   g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
 71s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu idseq-bench insilicoseq
 71s   libasan8 libblas3 libcairo2 libcc1-0 libdeflate0 libfontconfig1 libfontenc1
 71s   libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64
 71s   libhtscodecs2 libhwasan0 libimagequant0 libisl23 libitm1 libjbig0
 71s   libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblsan0
 71s   libmpc3 libopenjp2-7 libpixman-1-0 libpython3.13-minimal
 71s   libpython3.13-stdlib libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev
 71s   libtiff6 libtsan2 libubsan1 libwebp7 libwebpdemux2 libwebpmux3
 71s   libxcb-render0 libxcb-shm0 libxrender1 ncbi-acc-download python3-all
 71s   python3-biopython python3-cairo python3-decorator python3-freetype
 71s   python3-joblib python3-numpy python3-pil python3-pysam python3-reportlab
 71s   python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib
 71s   python3-smart-open python3-threadpoolctl python3-wrapt python3.13
 71s   python3.13-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings
 71s   xfonts-utils xml-core
 71s 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded.
 71s Need to get 133 MB of archives.
 71s After this operation, 490 MB of additional disk space will be used.
 71s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
 71s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
 71s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB]
 71s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
 71s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
 71s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
 72s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
 72s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
 72s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
 72s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
 72s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 72s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
 72s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
 72s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
 72s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
 72s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
 72s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
 72s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
 72s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
 72s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
 73s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
 73s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
 73s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
 73s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
 73s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
 74s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
 74s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
 74s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
 74s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
 74s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
 74s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
 74s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB]
 74s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
 74s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
 74s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB]
 74s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
 74s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
 74s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
 74s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
 74s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
 74s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
 74s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
 74s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
 74s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
 74s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB]
 74s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB]
 74s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
 74s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
 74s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
 74s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
 74s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
 74s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
 74s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
 74s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
 74s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
 74s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
 74s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
 74s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB]
 74s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
 74s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
 75s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
 75s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
 75s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
 75s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
 75s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB]
 75s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB]
 75s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B]
 75s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB]
 75s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB]
 75s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
 75s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB]
 75s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB]
 75s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB]
 75s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB]
 75s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
 75s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
 75s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
 75s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 insilicoseq all 2.0.1-1 [4247 kB]
 75s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-acc-download all 0.2.8-3 [13.3 kB]
 75s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB]
 75s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB]
 75s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB]
 76s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
 76s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-wrapt amd64 1.15.0-3 [34.6 kB]
 76s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-smart-open all 7.0.5-1 [89.9 kB]
 76s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 idseq-bench all 0.0~git20210602.27fb6dc-1 [24.7 kB]
 76s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
 76s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
 76s Get:89 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
 76s Fetched 133 MB in 5s (26.3 MB/s)
 76s Selecting previously unselected package libpython3.13-minimal:amd64.
 76s (Reading database ... 
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(Reading database ... 10%
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(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%
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 83s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
 83s Setting up liblapack3:amd64 (3.12.0-3build2) ...
 83s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
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 84s Setting up xfonts-utils (1:7.7+7) ...
 84s Setting up libraqm0:amd64 (0.10.1-1build1) ...
 84s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
 84s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
 87s Setting up cpp-14 (14.2.0-8ubuntu1) ...
 87s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
 87s Setting up xml-core (0.19) ...
 87s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
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 87s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
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 98s Setting up gcc (4:14.1.0-2ubuntu1) ...
 98s Setting up g++ (4:14.1.0-2ubuntu1) ...
 98s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
 98s Setting up build-essential (12.10ubuntu1) ...
 98s Processing triggers for libc-bin (2.40-1ubuntu3) ...
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 98s Setting up w3c-sgml-lib (1.3-3) ...
121s Setting up python3-biopython (1.84+dfsg-4) ...
123s Setting up insilicoseq (2.0.1-1) ...
123s Setting up idseq-bench (0.0~git20210602.27fb6dc-1) ...
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
125s Starting pkgProblemResolver with broken count: 0
125s Starting 2 pkgProblemResolver with broken count: 0
125s Done
125s The following NEW packages will be installed:
125s   autopkgtest-satdep
125s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
125s Need to get 0 B/700 B of archives.
125s After this operation, 0 B of additional disk space will be used.
125s Get:1 /tmp/autopkgtest.j1wxzW/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [700 B]
125s Selecting previously unselected package autopkgtest-satdep.
125s (Reading database ... 
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125s Preparing to unpack .../2-autopkgtest-satdep.deb ...
125s Unpacking autopkgtest-satdep (0) ...
125s Setting up autopkgtest-satdep (0) ...
127s (Reading database ... 83859 files and directories currently installed.)
127s Removing autopkgtest-satdep (0) ...
128s autopkgtest [13:03:18]: test run-unit-test: [-----------------------
378s INFO:iss.app:Starting iss generate
378s INFO:iss.generator:Using kde ErrorModel
378s INFO:iss.util:Stitching input files together
378s INFO:iss.generator:Using abundance file:norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_5038_abundance.txt
378s INFO:iss.app:Using 2 cpus for read generation
378s INFO:iss.app:Generating 60000 reads
399s INFO:iss.util:Stitching input files together
399s INFO:iss.util:Stitching input files together
399s INFO:iss.util:Cleaning up
399s INFO:iss.app:Read generation complete
405s Generating IDseq benchmark data...
405s 'cd downloads; ncbi-acc-download --format fasta NC_016845.1 -e all'
405s 'cat downloads/NC_016845.1.fa > downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta'
405s "grep -v '^>' downloads/bateria__klebsiella_pneumoniae_HS11286__1125630.fasta | tr -d '\n' | wc > bateria__klebsiella_pneumoniae_HS11286__1125630.size"
405s Genome bateria__klebsiella_pneumoniae_HS11286__1125630 size 5333942 bases.
405s 'cd downloads; ncbi-acc-download --format fasta NC_007194.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007195.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007196.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007197.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007198.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007199.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007200.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_007201.1 -e all'
405s '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'
405s "grep -v '^>' downloads/fungi__aspergillus_fumigatus__330879.fasta | tr -d '\n' | wc > fungi__aspergillus_fumigatus__330879.size"
405s Genome fungi__aspergillus_fumigatus__330879 size 29384958 bases.
405s 'cd downloads; ncbi-acc-download --format fasta MG148341.1 -e all'
405s 'cat downloads/MG148341.1.fa > downloads/viruses__rhinovirus_c__463676.fasta'
405s "grep -v '^>' downloads/viruses__rhinovirus_c__463676.fasta | tr -d '\n' | wc > viruses__rhinovirus_c__463676.size"
405s Genome viruses__rhinovirus_c__463676 size 7056 bases.
405s 'cd downloads; ncbi-acc-download --format fasta MG049915.1 -e all'
405s 'cat downloads/MG049915.1.fa > downloads/viruses__chikungunya__37124.fasta'
405s "grep -v '^>' downloads/viruses__chikungunya__37124.fasta | tr -d '\n' | wc > viruses__chikungunya__37124.size"
405s Genome viruses__chikungunya__37124 size 11604 bases.
405s 'cd downloads; ncbi-acc-download --format fasta NC_007795.1 -e all'
405s 'cat downloads/NC_007795.1.fa > downloads/bateria__staphylococcus_aureus__93061.fasta'
405s "grep -v '^>' downloads/bateria__staphylococcus_aureus__93061.fasta | tr -d '\n' | wc > bateria__staphylococcus_aureus__93061.size"
405s Genome bateria__staphylococcus_aureus__93061 size 2821361 bases.
405s 'cd downloads; ncbi-acc-download --format fasta NC_004325.2 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_037280.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_000521.4 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004318.2 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004326.2 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004327.3 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004328.3 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004329.3 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004330.2 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_037281.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_037282.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_037284.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_004331.3 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_037283.1 -e all'
405s 'cd downloads; ncbi-acc-download --format fasta NC_036769.1 -e all'
405s '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'
405s "grep -v '^>' downloads/protista__plasmodium_falciuparum__36329.fasta | tr -d '\n' | wc > protista__plasmodium_falciuparum__36329.size"
405s Genome protista__plasmodium_falciuparum__36329 size 23326872 bases.
405s Initializing and downloading genomes...
405s GENERATING norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6
405s 'iss --version > iss_version.txt'
405s '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_5038_genomes.fasta'
405s 'iss generate --n_reads 60000 --genomes norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_5038_genomes.fasta --model hiseq --abundance_file norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_5038_abundance.txt --gc_bias --output norg_6__nacc_27__uniform_weight_per_organism__hiseq_reads__v0.2.6/tmp_5038 --cpus 2'
405s *** 100.0 percent done, 0.5 minutes elapsed, 0.0 minutes remaining, ETA 13:07:55 ***
405s 
405s autopkgtest [13:07:55]: test run-unit-test: -----------------------]
406s autopkgtest [13:07:56]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
406s run-unit-test        PASS
406s autopkgtest [13:07:56]: @@@@@@@@@@@@@@@@@@@@ summary
406s run-unit-test        PASS
418s nova [W] Skipping flock for amd64
418s Creating nova instance adt-plucky-i386-idseq-bench-20241114-130110-juju-7f2275-prod-proposed-migration-environment-15-0a245cfe-9b22-437f-a992-c7cc330b9d81 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...