0s autopkgtest [18:38:31]: starting date and time: 2024-03-18 18:38:31+0000
  0s autopkgtest [18:38:31]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [18:38:31]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dqzc7v2c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade virulencefinder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-8.secgroup --name adt-noble-ppc64el-virulencefinder-20240318-183831-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/
234s autopkgtest [18:42:25]: testbed dpkg architecture: ppc64el
234s autopkgtest [18:42:25]: testbed apt version: 2.7.12
234s autopkgtest [18:42:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup
236s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
236s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB]
236s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
236s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
236s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3720 kB]
237s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [643 kB]
237s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
237s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
237s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
237s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4012 kB]
238s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
238s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [48.4 kB]
238s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
241s Fetched 9098 kB in 3s (3036 kB/s)
241s Reading package lists...
244s Reading package lists...
244s Building dependency tree...
244s Reading state information...
244s Calculating upgrade...
244s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
244s Reading package lists...
244s Building dependency tree...
244s Reading state information...
245s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
245s sh: Attempting to set up Debian/Ubuntu apt sources automatically
245s sh: Distribution appears to be Ubuntu
246s Reading package lists...
246s Building dependency tree...
246s Reading state information...
247s eatmydata is already the newest version (131-1).
247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
247s Reading package lists...
247s Building dependency tree...
247s Reading state information...
247s dbus is already the newest version (1.14.10-4ubuntu1).
247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
247s Reading package lists...
247s Building dependency tree...
247s Reading state information...
247s rng-tools-debian is already the newest version (2.4).
247s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
247s Reading package lists...
248s Building dependency tree...
248s Reading state information...
248s The following packages will be REMOVED:
248s   cloud-init* python3-configobj* python3-debconf*
248s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
248s After this operation, 3252 kB disk space will be freed.
248s (Reading database ... 
(Reading database ... 5%
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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 ... 70095 files and directories currently installed.)
248s Removing cloud-init (24.1.1-0ubuntu1) ...
249s Removing python3-configobj (5.0.8-3) ...
249s Removing python3-debconf (1.5.86) ...
249s Processing triggers for man-db (2.12.0-3) ...
249s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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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 ... 69706 files and directories currently installed.)
249s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ...
250s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
250s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
250s invoke-rc.d: policy-rc.d denied execution of try-restart.
250s Reading package lists...
250s Building dependency tree...
250s Reading state information...
250s linux-generic is already the newest version (6.8.0-11.11+1).
250s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
251s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
251s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
251s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
254s Reading package lists...
254s Reading package lists...
254s Building dependency tree...
254s Reading state information...
254s Calculating upgrade...
254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
254s Reading package lists...
254s Building dependency tree...
254s Reading state information...
254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
255s autopkgtest [18:42:46]: rebooting testbed after setup commands that affected boot
423s autopkgtest [18:45:34]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
425s autopkgtest [18:45:36]: @@@@@@@@@@@@@@@@@@@@ apt-source virulencefinder
428s Get:1 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (dsc) [2273 B]
428s Get:2 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (tar) [264 kB]
428s Get:3 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (diff) [6148 B]
428s gpgv: Signature made Sat Mar  9 11:28:05 2024 UTC
428s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
428s gpgv: Can't check signature: No public key
428s dpkg-source: warning: cannot verify inline signature for ./virulencefinder_2.0.5-1ubuntu1.dsc: no acceptable signature found
428s autopkgtest [18:45:39]: testing package virulencefinder version 2.0.5-1ubuntu1
428s autopkgtest [18:45:39]: build not needed
447s autopkgtest [18:45:58]: test run-unit-test: preparing testbed
450s Reading package lists...
450s Building dependency tree...
450s Reading state information...
450s Starting pkgProblemResolver with broken count: 0
450s Starting 2 pkgProblemResolver with broken count: 0
450s Done
451s The following additional packages will be installed:
451s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
451s   fonts-urw-base35 kma libblas3 libcairo2 libdeflate0 libfontconfig1
451s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
451s   libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2
451s   liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libopenjp2-7
451s   libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
451s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data
451s   python3-biopython python3-cairo python3-cgecore python3-freetype
451s   python3-numpy python3-pil python3-reportlab python3-rlpycairo
451s   python3-tabulate sgml-base virulencefinder virulencefinder-examples
451s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
451s Suggested packages:
451s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
451s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
451s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
451s   python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
451s   gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer
451s   python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
451s   sgml-base-doc debhelper
451s Recommended packages:
451s   python-biopython-doc python3-olefile
451s The following NEW packages will be installed:
451s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra
451s   fonts-dejavu-mono fonts-urw-base35 kma libblas3 libcairo2 libdeflate0
451s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
451s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
451s   liblcms2-2 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libopenjp2-7
451s   libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
451s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data
451s   python3-biopython python3-cairo python3-cgecore python3-freetype
451s   python3-numpy python3-pil python3-reportlab python3-rlpycairo
451s   python3-tabulate sgml-base virulencefinder virulencefinder-examples
451s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
451s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded.
451s Need to get 50.5 MB/50.5 MB of archives.
451s After this operation, 198 MB of additional disk space will be used.
451s Get:1 /tmp/autopkgtest.0QqCeE/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
451s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB]
451s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
451s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
452s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontenc1 ppc64el 1:1.1.8-1 [15.7 kB]
452s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB]
452s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
452s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el xfonts-utils ppc64el 1:7.7+6build2 [112 kB]
452s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB]
454s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el fontconfig-config ppc64el 2.15.0-1ubuntu1 [37.0 kB]
454s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-dejavu-extra all 2.37-8 [1947 kB]
454s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el kma ppc64el 1.4.14-2 [270 kB]
454s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB]
454s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libfontconfig1 ppc64el 2.15.0-1ubuntu1 [190 kB]
454s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el libpixman-1-0 ppc64el 0.42.2-1 [300 kB]
454s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-render0 ppc64el 1.15-1 [17.2 kB]
454s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B]
454s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1 [23.3 kB]
454s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libcairo2 ppc64el 1.18.0-1 [735 kB]
454s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB]
454s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB]
454s Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB]
454s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libgraphite2-3 ppc64el 1.3.14-2 [105 kB]
454s Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libharfbuzz0b ppc64el 8.3.0-2 [576 kB]
454s Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libimagequant0 ppc64el 2.18.0-1 [42.5 kB]
454s Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB]
454s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
454s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB]
455s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el liblcms2-2 ppc64el 2.14-2 [243 kB]
455s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB]
455s Get:31 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedcrypto7 ppc64el 2.28.7-1ubuntu1 [262 kB]
455s Get:32 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedx509-1 ppc64el 2.28.7-1ubuntu1 [51.4 kB]
455s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmbedtls14 ppc64el 2.28.7-1ubuntu1 [89.7 kB]
455s Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libraqm0 ppc64el 0.10.1-1 [18.9 kB]
455s Get:35 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB]
455s Get:36 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB]
455s Get:37 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB]
455s Get:38 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB]
455s Get:39 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpdemux2 ppc64el 1.3.2-0.4 [14.4 kB]
455s Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebpmux3 ppc64el 1.3.2-0.4 [31.2 kB]
455s Get:41 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
455s Get:42 http://ftpmaster.internal/ubuntu noble/universe ppc64el ncbi-blast+ ppc64el 2.12.0+ds-4 [13.4 MB]
456s Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB]
456s Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libopenjp2-7 ppc64el 2.5.0-2 [233 kB]
456s Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-pil ppc64el 10.2.0-1 [526 kB]
456s Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-cairo ppc64el 1.25.1-2 [162 kB]
456s Get:47 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-freetype all 2.4.0-1 [83.1 kB]
456s Get:48 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B]
456s Get:49 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-reportlab all 4.1.0-1 [683 kB]
456s Get:50 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB]
456s Get:51 http://ftpmaster.internal/ubuntu noble/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB]
456s Get:52 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biopython ppc64el 1.81+dfsg-3 [1738 kB]
456s Get:53 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-cgecore all 1.5.6+ds-1 [28.8 kB]
456s Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-tabulate all 0.8.10-1 [38.2 kB]
456s Get:55 http://ftpmaster.internal/ubuntu noble/universe ppc64el virulencefinder all 2.0.5-1ubuntu1 [13.7 kB]
456s Get:56 http://ftpmaster.internal/ubuntu noble/universe ppc64el virulencefinder-examples all 2.0.5-1ubuntu1 [373 kB]
456s Fetched 50.5 MB in 5s (9468 kB/s)
456s Selecting previously unselected package sgml-base.
456s (Reading database ... 
(Reading database ... 5%
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(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 ... 69651 files and directories currently installed.)
456s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
456s Unpacking sgml-base (1.31) ...
456s Selecting previously unselected package fonts-dejavu-mono.
456s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
456s Unpacking fonts-dejavu-mono (2.37-8) ...
456s Selecting previously unselected package fonts-dejavu-core.
456s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
456s Unpacking fonts-dejavu-core (2.37-8) ...
456s Selecting previously unselected package libfontenc1:ppc64el.
456s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_ppc64el.deb ...
456s Unpacking libfontenc1:ppc64el (1:1.1.8-1) ...
456s Selecting previously unselected package x11-common.
456s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu2_all.deb ...
456s Unpacking x11-common (1:7.7+23ubuntu2) ...
456s Selecting previously unselected package xfonts-encodings.
456s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
456s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
456s Selecting previously unselected package xfonts-utils.
456s Preparing to unpack .../06-xfonts-utils_1%3a7.7+6build2_ppc64el.deb ...
456s Unpacking xfonts-utils (1:7.7+6build2) ...
456s Selecting previously unselected package fonts-urw-base35.
456s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ...
457s Unpacking fonts-urw-base35 (20200910-8) ...
457s Selecting previously unselected package fontconfig-config.
457s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_ppc64el.deb ...
457s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
457s Selecting previously unselected package fonts-dejavu-extra.
457s Preparing to unpack .../09-fonts-dejavu-extra_2.37-8_all.deb ...
457s Unpacking fonts-dejavu-extra (2.37-8) ...
457s Selecting previously unselected package kma.
457s Preparing to unpack .../10-kma_1.4.14-2_ppc64el.deb ...
457s Unpacking kma (1.4.14-2) ...
457s Selecting previously unselected package libblas3:ppc64el.
457s Preparing to unpack .../11-libblas3_3.12.0-3_ppc64el.deb ...
457s Unpacking libblas3:ppc64el (3.12.0-3) ...
457s Selecting previously unselected package libfontconfig1:ppc64el.
457s Preparing to unpack .../12-libfontconfig1_2.15.0-1ubuntu1_ppc64el.deb ...
457s Unpacking libfontconfig1:ppc64el (2.15.0-1ubuntu1) ...
457s Selecting previously unselected package libpixman-1-0:ppc64el.
457s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_ppc64el.deb ...
457s Unpacking libpixman-1-0:ppc64el (0.42.2-1) ...
457s Selecting previously unselected package libxcb-render0:ppc64el.
457s Preparing to unpack .../14-libxcb-render0_1.15-1_ppc64el.deb ...
457s Unpacking libxcb-render0:ppc64el (1.15-1) ...
457s Selecting previously unselected package libxcb-shm0:ppc64el.
457s Preparing to unpack .../15-libxcb-shm0_1.15-1_ppc64el.deb ...
457s Unpacking libxcb-shm0:ppc64el (1.15-1) ...
457s Selecting previously unselected package libxrender1:ppc64el.
457s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_ppc64el.deb ...
457s Unpacking libxrender1:ppc64el (1:0.9.10-1.1) ...
457s Selecting previously unselected package libcairo2:ppc64el.
457s Preparing to unpack .../17-libcairo2_1.18.0-1_ppc64el.deb ...
457s Unpacking libcairo2:ppc64el (1.18.0-1) ...
457s Selecting previously unselected package libdeflate0:ppc64el.
457s Preparing to unpack .../18-libdeflate0_1.19-1_ppc64el.deb ...
457s Unpacking libdeflate0:ppc64el (1.19-1) ...
457s Selecting previously unselected package libgfortran5:ppc64el.
457s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ...
457s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
457s Selecting previously unselected package libgomp1:ppc64el.
457s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ...
457s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ...
457s Selecting previously unselected package libgraphite2-3:ppc64el.
457s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_ppc64el.deb ...
457s Unpacking libgraphite2-3:ppc64el (1.3.14-2) ...
457s Selecting previously unselected package libharfbuzz0b:ppc64el.
457s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_ppc64el.deb ...
457s Unpacking libharfbuzz0b:ppc64el (8.3.0-2) ...
457s Selecting previously unselected package libimagequant0:ppc64el.
457s Preparing to unpack .../23-libimagequant0_2.18.0-1_ppc64el.deb ...
457s Unpacking libimagequant0:ppc64el (2.18.0-1) ...
457s Selecting previously unselected package libjpeg-turbo8:ppc64el.
457s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ...
457s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ...
457s Selecting previously unselected package libjpeg8:ppc64el.
457s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_ppc64el.deb ...
457s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ...
457s Selecting previously unselected package liblapack3:ppc64el.
457s Preparing to unpack .../26-liblapack3_3.12.0-3_ppc64el.deb ...
457s Unpacking liblapack3:ppc64el (3.12.0-3) ...
457s Selecting previously unselected package liblcms2-2:ppc64el.
457s Preparing to unpack .../27-liblcms2-2_2.14-2_ppc64el.deb ...
457s Unpacking liblcms2-2:ppc64el (2.14-2) ...
457s Selecting previously unselected package liblerc4:ppc64el.
457s Preparing to unpack .../28-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ...
457s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ...
457s Selecting previously unselected package libmbedcrypto7:ppc64el.
457s Preparing to unpack .../29-libmbedcrypto7_2.28.7-1ubuntu1_ppc64el.deb ...
457s Unpacking libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ...
457s Selecting previously unselected package libmbedx509-1:ppc64el.
457s Preparing to unpack .../30-libmbedx509-1_2.28.7-1ubuntu1_ppc64el.deb ...
457s Unpacking libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ...
457s Selecting previously unselected package libmbedtls14:ppc64el.
457s Preparing to unpack .../31-libmbedtls14_2.28.7-1ubuntu1_ppc64el.deb ...
457s Unpacking libmbedtls14:ppc64el (2.28.7-1ubuntu1) ...
457s Selecting previously unselected package libraqm0:ppc64el.
457s Preparing to unpack .../32-libraqm0_0.10.1-1_ppc64el.deb ...
457s Unpacking libraqm0:ppc64el (0.10.1-1) ...
457s Selecting previously unselected package libsharpyuv0:ppc64el.
457s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_ppc64el.deb ...
457s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ...
457s Selecting previously unselected package libjbig0:ppc64el.
457s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ...
457s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ...
457s Selecting previously unselected package libwebp7:ppc64el.
457s Preparing to unpack .../35-libwebp7_1.3.2-0.4_ppc64el.deb ...
457s Unpacking libwebp7:ppc64el (1.3.2-0.4) ...
457s Selecting previously unselected package libtiff6:ppc64el.
457s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ...
457s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ...
457s Selecting previously unselected package libwebpdemux2:ppc64el.
457s Preparing to unpack .../37-libwebpdemux2_1.3.2-0.4_ppc64el.deb ...
457s Unpacking libwebpdemux2:ppc64el (1.3.2-0.4) ...
457s Selecting previously unselected package libwebpmux3:ppc64el.
457s Preparing to unpack .../38-libwebpmux3_1.3.2-0.4_ppc64el.deb ...
457s Unpacking libwebpmux3:ppc64el (1.3.2-0.4) ...
457s Selecting previously unselected package ncbi-data.
457s Preparing to unpack .../39-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
457s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
458s Selecting previously unselected package ncbi-blast+.
458s Preparing to unpack .../40-ncbi-blast+_2.12.0+ds-4_ppc64el.deb ...
458s Unpacking ncbi-blast+ (2.12.0+ds-4) ...
458s Selecting previously unselected package python3-numpy.
458s Preparing to unpack .../41-python3-numpy_1%3a1.24.2-2_ppc64el.deb ...
458s Unpacking python3-numpy (1:1.24.2-2) ...
458s Selecting previously unselected package libopenjp2-7:ppc64el.
458s Preparing to unpack .../42-libopenjp2-7_2.5.0-2_ppc64el.deb ...
458s Unpacking libopenjp2-7:ppc64el (2.5.0-2) ...
458s Selecting previously unselected package python3-pil:ppc64el.
458s Preparing to unpack .../43-python3-pil_10.2.0-1_ppc64el.deb ...
458s Unpacking python3-pil:ppc64el (10.2.0-1) ...
458s Selecting previously unselected package python3-cairo.
458s Preparing to unpack .../44-python3-cairo_1.25.1-2_ppc64el.deb ...
458s Unpacking python3-cairo (1.25.1-2) ...
458s Selecting previously unselected package python3-freetype.
458s Preparing to unpack .../45-python3-freetype_2.4.0-1_all.deb ...
458s Unpacking python3-freetype (2.4.0-1) ...
458s Selecting previously unselected package python3-rlpycairo.
458s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ...
458s Unpacking python3-rlpycairo (0.3.0-3) ...
458s Selecting previously unselected package python3-reportlab.
458s Preparing to unpack .../47-python3-reportlab_4.1.0-1_all.deb ...
458s Unpacking python3-reportlab (4.1.0-1) ...
458s Selecting previously unselected package xml-core.
458s Preparing to unpack .../48-xml-core_0.19_all.deb ...
458s Unpacking xml-core (0.19) ...
458s Selecting previously unselected package w3c-sgml-lib.
458s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ...
458s Unpacking w3c-sgml-lib (1.3-3) ...
459s Selecting previously unselected package python3-biopython.
459s Preparing to unpack .../50-python3-biopython_1.81+dfsg-3_ppc64el.deb ...
459s Unpacking python3-biopython (1.81+dfsg-3) ...
459s Selecting previously unselected package python3-cgecore.
459s Preparing to unpack .../51-python3-cgecore_1.5.6+ds-1_all.deb ...
459s Unpacking python3-cgecore (1.5.6+ds-1) ...
459s Selecting previously unselected package python3-tabulate.
459s Preparing to unpack .../52-python3-tabulate_0.8.10-1_all.deb ...
459s Unpacking python3-tabulate (0.8.10-1) ...
459s Selecting previously unselected package virulencefinder.
459s Preparing to unpack .../53-virulencefinder_2.0.5-1ubuntu1_all.deb ...
459s Unpacking virulencefinder (2.0.5-1ubuntu1) ...
459s Selecting previously unselected package virulencefinder-examples.
459s Preparing to unpack .../54-virulencefinder-examples_2.0.5-1ubuntu1_all.deb ...
459s Unpacking virulencefinder-examples (2.0.5-1ubuntu1) ...
459s Selecting previously unselected package autopkgtest-satdep.
459s Preparing to unpack .../55-1-autopkgtest-satdep.deb ...
459s Unpacking autopkgtest-satdep (0) ...
459s Setting up libgraphite2-3:ppc64el (1.3.14-2) ...
459s Setting up liblcms2-2:ppc64el (2.14-2) ...
459s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
459s Setting up libpixman-1-0:ppc64el (0.42.2-1) ...
459s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ...
459s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ...
459s Setting up libxrender1:ppc64el (1:0.9.10-1.1) ...
459s Setting up libxcb-render0:ppc64el (1.15-1) ...
459s Setting up x11-common (1:7.7+23ubuntu2) ...
459s Setting up libdeflate0:ppc64el (1.19-1) ...
459s Setting up python3-tabulate (0.8.10-1) ...
459s Setting up virulencefinder-examples (2.0.5-1ubuntu1) ...
459s Setting up libxcb-shm0:ppc64el (1.15-1) ...
459s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ...
459s Setting up python3-freetype (2.4.0-1) ...
460s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ...
460s Setting up libfontenc1:ppc64el (1:1.1.8-1) ...
460s Setting up libblas3:ppc64el (3.12.0-3) ...
460s 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
460s Setting up libmbedcrypto7:ppc64el (2.28.7-1ubuntu1) ...
460s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
460s Setting up libimagequant0:ppc64el (2.18.0-1) ...
460s Setting up fonts-dejavu-mono (2.37-8) ...
460s Setting up fonts-dejavu-core (2.37-8) ...
460s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ...
460s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
460s Setting up libwebp7:ppc64el (1.3.2-0.4) ...
460s Setting up fonts-dejavu-extra (2.37-8) ...
460s Setting up kma (1.4.14-2) ...
460s Setting up libopenjp2-7:ppc64el (2.5.0-2) ...
460s Setting up libharfbuzz0b:ppc64el (8.3.0-2) ...
460s Setting up sgml-base (1.31) ...
460s Setting up libwebpmux3:ppc64el (1.3.2-0.4) ...
460s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
460s Setting up liblapack3:ppc64el (3.12.0-3) ...
460s 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
460s Setting up libmbedx509-1:ppc64el (2.28.7-1ubuntu1) ...
460s Setting up libmbedtls14:ppc64el (2.28.7-1ubuntu1) ...
460s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
460s Setting up libwebpdemux2:ppc64el (1.3.2-0.4) ...
460s Setting up xfonts-utils (1:7.7+6build2) ...
460s Setting up ncbi-blast+ (2.12.0+ds-4) ...
460s Setting up libraqm0:ppc64el (0.10.1-1) ...
460s Setting up python3-numpy (1:1.24.2-2) ...
462s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ...
462s Setting up xml-core (0.19) ...
462s Setting up libfontconfig1:ppc64el (2.15.0-1ubuntu1) ...
462s Setting up fonts-urw-base35 (20200910-8) ...
462s Setting up libcairo2:ppc64el (1.18.0-1) ...
462s Setting up python3-pil:ppc64el (10.2.0-1) ...
462s Setting up python3-cairo (1.25.1-2) ...
462s Setting up python3-rlpycairo (0.3.0-3) ...
463s Setting up python3-reportlab (4.1.0-1) ...
463s Processing triggers for libc-bin (2.39-0ubuntu2) ...
463s Processing triggers for man-db (2.12.0-3) ...
464s Processing triggers for sgml-base (1.31) ...
464s Setting up w3c-sgml-lib (1.3-3) ...
492s Setting up python3-biopython (1.81+dfsg-3) ...
494s Setting up python3-cgecore (1.5.6+ds-1) ...
494s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
494s   start = re.search("^-*(\w+)", align_query).start(1)
494s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
494s   end = re.search("\w+(-*)$", align_query).start(1)
494s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
494s   """
494s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
494s   src = re.sub('[^\w/\-\.\*]', '', src)
494s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
494s   dst = re.sub('[^\w/\-\.\*]', '', dst)
494s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
494s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
494s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
494s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
494s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
494s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
494s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
494s   src = re.sub('[^\w/\-\.\*]', '', src)
494s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
494s   dst = re.sub('[^\w/\-\.\*]', '', dst)
494s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
494s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
494s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
494s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
494s Setting up virulencefinder (2.0.5-1ubuntu1) ...
494s Setting up autopkgtest-satdep (0) ...
497s (Reading database ... 73223 files and directories currently installed.)
497s Removing autopkgtest-satdep (0) ...
498s autopkgtest [18:46:49]: test run-unit-test: [-----------------------
499s TEST SUCCEEDED
499s autopkgtest [18:46:50]: test run-unit-test: -----------------------]
500s run-unit-test        PASS
500s autopkgtest [18:46:51]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
500s autopkgtest [18:46:51]: @@@@@@@@@@@@@@@@@@@@ summary
500s run-unit-test        PASS
533s Creating nova instance adt-noble-ppc64el-virulencefinder-20240318-183831-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 1492b190-05c5-462d-b1de-84bc330afe32)...