0s autopkgtest [22:30:57]: starting date and time: 2024-03-17 22:30:57+0000
  0s autopkgtest [22:30:57]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [22:30:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y4wvuoki/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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-2@bos02-s390x-10.secgroup --name adt-noble-s390x-virulencefinder-20240317-223057-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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://ftpmaster.internal/ubuntu/
152s autopkgtest [22:33:29]: testbed dpkg architecture: s390x
152s autopkgtest [22:33:29]: testbed apt version: 2.7.12
152s autopkgtest [22:33:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup
153s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
153s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
153s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
153s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3691 kB]
153s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
153s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [639 kB]
153s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
153s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B]
153s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
153s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3878 kB]
153s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
153s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [33.2 kB]
153s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
155s Fetched 8913 kB in 2s (4000 kB/s)
156s Reading package lists...
158s Reading package lists...
158s Building dependency tree...
158s Reading state information...
158s Calculating upgrade...
158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
158s Reading package lists...
159s Building dependency tree...
159s Reading state information...
159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
159s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
159s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
159s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
159s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
160s Reading package lists...
160s Reading package lists...
160s Building dependency tree...
160s Reading state information...
161s Calculating upgrade...
161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
161s Reading package lists...
161s Building dependency tree...
161s Reading state information...
161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
164s autopkgtest [22:33:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024
164s autopkgtest [22:33:41]: @@@@@@@@@@@@@@@@@@@@ apt-source virulencefinder
166s Get:1 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (dsc) [2273 B]
166s Get:2 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (tar) [264 kB]
166s Get:3 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (diff) [6148 B]
166s gpgv: Signature made Sat Mar  9 11:28:05 2024 UTC
166s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
166s gpgv: Can't check signature: No public key
166s dpkg-source: warning: cannot verify inline signature for ./virulencefinder_2.0.5-1ubuntu1.dsc: no acceptable signature found
166s autopkgtest [22:33:43]: testing package virulencefinder version 2.0.5-1ubuntu1
166s autopkgtest [22:33:43]: build not needed
167s autopkgtest [22:33:44]: test run-unit-test: preparing testbed
168s Reading package lists...
168s Building dependency tree...
168s Reading state information...
168s Starting pkgProblemResolver with broken count: 0
168s Starting 2 pkgProblemResolver with broken count: 0
168s Done
169s The following additional packages will be installed:
169s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
169s   fonts-urw-base35 kma libblas3 libcairo2 libdeflate0 libfontconfig1
169s   libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
169s   libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2
169s   libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libopenjp2-7
169s   libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
169s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data
169s   python3-biopython python3-cairo python3-cgecore python3-freetype
169s   python3-numpy python3-pil python3-reportlab python3-rlpycairo
169s   python3-tabulate sgml-base virulencefinder virulencefinder-examples
169s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
169s Suggested packages:
169s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
169s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
169s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
169s   python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
169s   gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer
169s   python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
169s   sgml-base-doc debhelper
169s Recommended packages:
169s   python-biopython-doc python3-olefile
169s The following NEW packages will be installed:
169s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra
169s   fonts-dejavu-mono fonts-urw-base35 kma libblas3 libcairo2 libdeflate0
169s   libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3
169s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
169s   liblcms2-2 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libopenjp2-7
169s   libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
169s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data
169s   python3-biopython python3-cairo python3-cgecore python3-freetype
169s   python3-numpy python3-pil python3-reportlab python3-rlpycairo
169s   python3-tabulate sgml-base virulencefinder virulencefinder-examples
169s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
169s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded.
169s Need to get 49.4 MB/49.4 MB of archives.
169s After this operation, 177 MB of additional disk space will be used.
169s Get:1 /tmp/autopkgtest.bGPbvW/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B]
169s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB]
169s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
169s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
169s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libfontenc1 s390x 1:1.1.8-1 [14.8 kB]
169s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libfreetype6 s390x 2.13.2+dfsg-1 [431 kB]
169s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x x11-common all 1:7.7+23ubuntu2 [23.4 kB]
169s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
169s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x xfonts-utils s390x 1:7.7+6build2 [94.8 kB]
169s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB]
170s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x fontconfig-config s390x 2.15.0-1ubuntu1 [37.0 kB]
170s Get:12 http://ftpmaster.internal/ubuntu noble/main s390x fonts-dejavu-extra all 2.37-8 [1947 kB]
170s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x kma s390x 1.4.14-2 [257 kB]
170s Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB]
170s Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libfontconfig1 s390x 2.15.0-1ubuntu1 [150 kB]
170s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libpixman-1-0 s390x 0.42.2-1 [173 kB]
170s Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-render0 s390x 1.15-1 [17.0 kB]
170s Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libxcb-shm0 s390x 1.15-1 [5782 B]
170s Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libxrender1 s390x 1:0.9.10-1.1 [19.4 kB]
170s Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libcairo2 s390x 1.18.0-1 [578 kB]
170s Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB]
170s Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB]
170s Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB]
170s Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libgraphite2-3 s390x 1.3.14-2 [90.4 kB]
170s Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libharfbuzz0b s390x 8.3.0-2 [515 kB]
170s Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libimagequant0 s390x 2.18.0-1 [42.9 kB]
170s Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu1 [128 kB]
170s Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
170s Get:29 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB]
170s Get:30 http://ftpmaster.internal/ubuntu noble/main s390x liblcms2-2 s390x 2.14-2 [155 kB]
170s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedcrypto7t64 s390x 2.28.7-1.1ubuntu1 [216 kB]
170s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedx509-1t64 s390x 2.28.7-1.1ubuntu1 [46.2 kB]
170s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libmbedtls14t64 s390x 2.28.7-1.1ubuntu1 [84.7 kB]
170s Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libraqm0 s390x 0.10.1-1 [14.4 kB]
170s Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libsharpyuv0 s390x 1.3.2-0.4 [14.8 kB]
170s Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libjbig0 s390x 2.1-6.1ubuntu1 [29.8 kB]
170s Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libwebp7 s390x 1.3.2-0.4 [207 kB]
170s Get:38 http://ftpmaster.internal/ubuntu noble/main s390x libtiff6 s390x 4.5.1+git230720-3ubuntu1 [253 kB]
170s Get:39 http://ftpmaster.internal/ubuntu noble/main s390x libwebpdemux2 s390x 1.3.2-0.4 [12.4 kB]
170s Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libwebpmux3 s390x 1.3.2-0.4 [25.4 kB]
170s Get:41 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
170s Get:42 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x ncbi-blast+ s390x 2.12.0+ds-4build1 [12.8 MB]
171s Get:43 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB]
171s Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libopenjp2-7 s390x 2.5.0-2 [169 kB]
171s Get:45 http://ftpmaster.internal/ubuntu noble/main s390x python3-pil s390x 10.2.0-1 [519 kB]
171s Get:46 http://ftpmaster.internal/ubuntu noble/main s390x python3-cairo s390x 1.25.1-2 [150 kB]
171s Get:47 http://ftpmaster.internal/ubuntu noble/universe s390x python3-freetype all 2.4.0-1 [83.1 kB]
171s Get:48 http://ftpmaster.internal/ubuntu noble/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B]
171s Get:49 http://ftpmaster.internal/ubuntu noble/universe s390x python3-reportlab all 4.1.0-1 [683 kB]
171s Get:50 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB]
171s Get:51 http://ftpmaster.internal/ubuntu noble/universe s390x w3c-sgml-lib all 1.3-3 [280 kB]
171s Get:52 http://ftpmaster.internal/ubuntu noble/universe s390x python3-biopython s390x 1.81+dfsg-3 [2234 kB]
171s Get:53 http://ftpmaster.internal/ubuntu noble/universe s390x python3-cgecore all 1.5.6+ds-1 [28.8 kB]
171s Get:54 http://ftpmaster.internal/ubuntu noble/main s390x python3-tabulate all 0.8.10-1 [38.2 kB]
171s Get:55 http://ftpmaster.internal/ubuntu noble/universe s390x virulencefinder all 2.0.5-1ubuntu1 [13.7 kB]
171s Get:56 http://ftpmaster.internal/ubuntu noble/universe s390x virulencefinder-examples all 2.0.5-1ubuntu1 [373 kB]
171s Fetched 49.4 MB in 2s (24.3 MB/s)
171s Selecting previously unselected package sgml-base.
171s (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 ... 52171 files and directories currently installed.)
171s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
171s Unpacking sgml-base (1.31) ...
171s Selecting previously unselected package fonts-dejavu-mono.
171s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ...
171s Unpacking fonts-dejavu-mono (2.37-8) ...
171s Selecting previously unselected package fonts-dejavu-core.
171s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ...
171s Unpacking fonts-dejavu-core (2.37-8) ...
171s Selecting previously unselected package libfontenc1:s390x.
171s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_s390x.deb ...
171s Unpacking libfontenc1:s390x (1:1.1.8-1) ...
171s Selecting previously unselected package libfreetype6:s390x.
171s Preparing to unpack .../04-libfreetype6_2.13.2+dfsg-1_s390x.deb ...
171s Unpacking libfreetype6:s390x (2.13.2+dfsg-1) ...
171s Selecting previously unselected package x11-common.
171s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ...
171s Unpacking x11-common (1:7.7+23ubuntu2) ...
171s Selecting previously unselected package xfonts-encodings.
171s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
171s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
171s Selecting previously unselected package xfonts-utils.
171s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_s390x.deb ...
171s Unpacking xfonts-utils (1:7.7+6build2) ...
171s Selecting previously unselected package fonts-urw-base35.
171s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ...
171s Unpacking fonts-urw-base35 (20200910-8) ...
172s Selecting previously unselected package fontconfig-config.
172s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_s390x.deb ...
172s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
172s Selecting previously unselected package fonts-dejavu-extra.
172s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ...
172s Unpacking fonts-dejavu-extra (2.37-8) ...
172s Selecting previously unselected package kma.
172s Preparing to unpack .../11-kma_1.4.14-2_s390x.deb ...
172s Unpacking kma (1.4.14-2) ...
172s Selecting previously unselected package libblas3:s390x.
172s Preparing to unpack .../12-libblas3_3.12.0-3_s390x.deb ...
172s Unpacking libblas3:s390x (3.12.0-3) ...
172s Selecting previously unselected package libfontconfig1:s390x.
172s Preparing to unpack .../13-libfontconfig1_2.15.0-1ubuntu1_s390x.deb ...
172s Unpacking libfontconfig1:s390x (2.15.0-1ubuntu1) ...
172s Selecting previously unselected package libpixman-1-0:s390x.
172s Preparing to unpack .../14-libpixman-1-0_0.42.2-1_s390x.deb ...
172s Unpacking libpixman-1-0:s390x (0.42.2-1) ...
172s Selecting previously unselected package libxcb-render0:s390x.
172s Preparing to unpack .../15-libxcb-render0_1.15-1_s390x.deb ...
172s Unpacking libxcb-render0:s390x (1.15-1) ...
172s Selecting previously unselected package libxcb-shm0:s390x.
172s Preparing to unpack .../16-libxcb-shm0_1.15-1_s390x.deb ...
172s Unpacking libxcb-shm0:s390x (1.15-1) ...
172s Selecting previously unselected package libxrender1:s390x.
172s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1_s390x.deb ...
172s Unpacking libxrender1:s390x (1:0.9.10-1.1) ...
172s Selecting previously unselected package libcairo2:s390x.
172s Preparing to unpack .../18-libcairo2_1.18.0-1_s390x.deb ...
172s Unpacking libcairo2:s390x (1.18.0-1) ...
172s Selecting previously unselected package libdeflate0:s390x.
172s Preparing to unpack .../19-libdeflate0_1.19-1_s390x.deb ...
172s Unpacking libdeflate0:s390x (1.19-1) ...
172s Selecting previously unselected package libgfortran5:s390x.
172s Preparing to unpack .../20-libgfortran5_14-20240303-1ubuntu1_s390x.deb ...
172s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ...
172s Selecting previously unselected package libgomp1:s390x.
172s Preparing to unpack .../21-libgomp1_14-20240303-1ubuntu1_s390x.deb ...
172s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ...
172s Selecting previously unselected package libgraphite2-3:s390x.
172s Preparing to unpack .../22-libgraphite2-3_1.3.14-2_s390x.deb ...
172s Unpacking libgraphite2-3:s390x (1.3.14-2) ...
172s Selecting previously unselected package libharfbuzz0b:s390x.
172s Preparing to unpack .../23-libharfbuzz0b_8.3.0-2_s390x.deb ...
172s Unpacking libharfbuzz0b:s390x (8.3.0-2) ...
172s Selecting previously unselected package libimagequant0:s390x.
172s Preparing to unpack .../24-libimagequant0_2.18.0-1_s390x.deb ...
172s Unpacking libimagequant0:s390x (2.18.0-1) ...
172s Selecting previously unselected package libjpeg-turbo8:s390x.
172s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu1_s390x.deb ...
172s Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ...
172s Selecting previously unselected package libjpeg8:s390x.
172s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_s390x.deb ...
172s Unpacking libjpeg8:s390x (8c-2ubuntu11) ...
172s Selecting previously unselected package liblapack3:s390x.
172s Preparing to unpack .../27-liblapack3_3.12.0-3_s390x.deb ...
172s Unpacking liblapack3:s390x (3.12.0-3) ...
172s Selecting previously unselected package liblcms2-2:s390x.
172s Preparing to unpack .../28-liblcms2-2_2.14-2_s390x.deb ...
172s Unpacking liblcms2-2:s390x (2.14-2) ...
172s Selecting previously unselected package libmbedcrypto7t64:s390x.
172s Preparing to unpack .../29-libmbedcrypto7t64_2.28.7-1.1ubuntu1_s390x.deb ...
172s Unpacking libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ...
172s Selecting previously unselected package libmbedx509-1t64:s390x.
172s Preparing to unpack .../30-libmbedx509-1t64_2.28.7-1.1ubuntu1_s390x.deb ...
172s Unpacking libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ...
172s Selecting previously unselected package libmbedtls14t64:s390x.
172s Preparing to unpack .../31-libmbedtls14t64_2.28.7-1.1ubuntu1_s390x.deb ...
172s Unpacking libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ...
172s Selecting previously unselected package libraqm0:s390x.
172s Preparing to unpack .../32-libraqm0_0.10.1-1_s390x.deb ...
172s Unpacking libraqm0:s390x (0.10.1-1) ...
172s Selecting previously unselected package libsharpyuv0:s390x.
172s Preparing to unpack .../33-libsharpyuv0_1.3.2-0.4_s390x.deb ...
172s Unpacking libsharpyuv0:s390x (1.3.2-0.4) ...
172s Selecting previously unselected package libjbig0:s390x.
172s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu1_s390x.deb ...
172s Unpacking libjbig0:s390x (2.1-6.1ubuntu1) ...
172s Selecting previously unselected package libwebp7:s390x.
172s Preparing to unpack .../35-libwebp7_1.3.2-0.4_s390x.deb ...
172s Unpacking libwebp7:s390x (1.3.2-0.4) ...
172s Selecting previously unselected package libtiff6:s390x.
172s Preparing to unpack .../36-libtiff6_4.5.1+git230720-3ubuntu1_s390x.deb ...
172s Unpacking libtiff6:s390x (4.5.1+git230720-3ubuntu1) ...
172s Selecting previously unselected package libwebpdemux2:s390x.
172s Preparing to unpack .../37-libwebpdemux2_1.3.2-0.4_s390x.deb ...
172s Unpacking libwebpdemux2:s390x (1.3.2-0.4) ...
172s Selecting previously unselected package libwebpmux3:s390x.
172s Preparing to unpack .../38-libwebpmux3_1.3.2-0.4_s390x.deb ...
172s Unpacking libwebpmux3:s390x (1.3.2-0.4) ...
172s Selecting previously unselected package ncbi-data.
172s Preparing to unpack .../39-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
172s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
172s Selecting previously unselected package ncbi-blast+.
172s Preparing to unpack .../40-ncbi-blast+_2.12.0+ds-4build1_s390x.deb ...
172s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ...
173s Selecting previously unselected package python3-numpy.
173s Preparing to unpack .../41-python3-numpy_1%3a1.24.2-2_s390x.deb ...
173s Unpacking python3-numpy (1:1.24.2-2) ...
173s Selecting previously unselected package libopenjp2-7:s390x.
173s Preparing to unpack .../42-libopenjp2-7_2.5.0-2_s390x.deb ...
173s Unpacking libopenjp2-7:s390x (2.5.0-2) ...
173s Selecting previously unselected package python3-pil:s390x.
173s Preparing to unpack .../43-python3-pil_10.2.0-1_s390x.deb ...
173s Unpacking python3-pil:s390x (10.2.0-1) ...
173s Selecting previously unselected package python3-cairo.
173s Preparing to unpack .../44-python3-cairo_1.25.1-2_s390x.deb ...
173s Unpacking python3-cairo (1.25.1-2) ...
173s Selecting previously unselected package python3-freetype.
173s Preparing to unpack .../45-python3-freetype_2.4.0-1_all.deb ...
173s Unpacking python3-freetype (2.4.0-1) ...
173s Selecting previously unselected package python3-rlpycairo.
173s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ...
173s Unpacking python3-rlpycairo (0.3.0-3) ...
173s Selecting previously unselected package python3-reportlab.
173s Preparing to unpack .../47-python3-reportlab_4.1.0-1_all.deb ...
173s Unpacking python3-reportlab (4.1.0-1) ...
173s Selecting previously unselected package xml-core.
173s Preparing to unpack .../48-xml-core_0.19_all.deb ...
173s Unpacking xml-core (0.19) ...
173s Selecting previously unselected package w3c-sgml-lib.
173s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ...
173s Unpacking w3c-sgml-lib (1.3-3) ...
173s Selecting previously unselected package python3-biopython.
173s Preparing to unpack .../50-python3-biopython_1.81+dfsg-3_s390x.deb ...
173s Unpacking python3-biopython (1.81+dfsg-3) ...
173s Selecting previously unselected package python3-cgecore.
173s Preparing to unpack .../51-python3-cgecore_1.5.6+ds-1_all.deb ...
173s Unpacking python3-cgecore (1.5.6+ds-1) ...
173s Selecting previously unselected package python3-tabulate.
173s Preparing to unpack .../52-python3-tabulate_0.8.10-1_all.deb ...
173s Unpacking python3-tabulate (0.8.10-1) ...
173s Selecting previously unselected package virulencefinder.
173s Preparing to unpack .../53-virulencefinder_2.0.5-1ubuntu1_all.deb ...
173s Unpacking virulencefinder (2.0.5-1ubuntu1) ...
173s Selecting previously unselected package virulencefinder-examples.
173s Preparing to unpack .../54-virulencefinder-examples_2.0.5-1ubuntu1_all.deb ...
173s Unpacking virulencefinder-examples (2.0.5-1ubuntu1) ...
173s Selecting previously unselected package autopkgtest-satdep.
173s Preparing to unpack .../55-1-autopkgtest-satdep.deb ...
173s Unpacking autopkgtest-satdep (0) ...
173s Setting up libgraphite2-3:s390x (1.3.14-2) ...
173s Setting up liblcms2-2:s390x (2.14-2) ...
173s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
173s Setting up libpixman-1-0:s390x (0.42.2-1) ...
173s Setting up libsharpyuv0:s390x (1.3.2-0.4) ...
173s Setting up libmbedcrypto7t64:s390x (2.28.7-1.1ubuntu1) ...
173s Setting up libxrender1:s390x (1:0.9.10-1.1) ...
173s Setting up libxcb-render0:s390x (1.15-1) ...
173s Setting up x11-common (1:7.7+23ubuntu2) ...
174s Setting up libdeflate0:s390x (1.19-1) ...
174s Setting up python3-tabulate (0.8.10-1) ...
174s Setting up virulencefinder-examples (2.0.5-1ubuntu1) ...
174s Setting up libxcb-shm0:s390x (1.15-1) ...
174s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ...
174s Setting up libjbig0:s390x (2.1-6.1ubuntu1) ...
174s Setting up libfontenc1:s390x (1:1.1.8-1) ...
174s Setting up libblas3:s390x (3.12.0-3) ...
174s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
174s Setting up libfreetype6:s390x (2.13.2+dfsg-1) ...
174s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
174s Setting up libimagequant0:s390x (2.18.0-1) ...
174s Setting up fonts-dejavu-mono (2.37-8) ...
174s Setting up fonts-dejavu-core (2.37-8) ...
174s Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu1) ...
174s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ...
174s Setting up libwebp7:s390x (1.3.2-0.4) ...
174s Setting up fonts-dejavu-extra (2.37-8) ...
174s Setting up kma (1.4.14-2) ...
174s Setting up libopenjp2-7:s390x (2.5.0-2) ...
174s Setting up libharfbuzz0b:s390x (8.3.0-2) ...
174s Setting up sgml-base (1.31) ...
174s Setting up libwebpmux3:s390x (1.3.2-0.4) ...
174s Setting up libjpeg8:s390x (8c-2ubuntu11) ...
174s Setting up liblapack3:s390x (3.12.0-3) ...
174s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
174s Setting up libmbedx509-1t64:s390x (2.28.7-1.1ubuntu1) ...
174s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
174s Setting up libwebpdemux2:s390x (1.3.2-0.4) ...
174s Setting up python3-freetype (2.4.0-1) ...
174s Setting up xfonts-utils (1:7.7+6build2) ...
174s Setting up libraqm0:s390x (0.10.1-1) ...
174s Setting up python3-numpy (1:1.24.2-2) ...
176s Setting up libmbedtls14t64:s390x (2.28.7-1.1ubuntu1) ...
176s Setting up libtiff6:s390x (4.5.1+git230720-3ubuntu1) ...
176s Setting up xml-core (0.19) ...
176s Setting up libfontconfig1:s390x (2.15.0-1ubuntu1) ...
176s Setting up fonts-urw-base35 (20200910-8) ...
176s Setting up libcairo2:s390x (1.18.0-1) ...
176s Setting up ncbi-blast+ (2.12.0+ds-4build1) ...
176s Setting up python3-pil:s390x (10.2.0-1) ...
176s Setting up python3-cairo (1.25.1-2) ...
177s Setting up python3-rlpycairo (0.3.0-3) ...
177s Setting up python3-reportlab (4.1.0-1) ...
177s Processing triggers for libc-bin (2.39-0ubuntu2) ...
177s Processing triggers for man-db (2.12.0-3) ...
178s Processing triggers for sgml-base (1.31) ...
178s Setting up w3c-sgml-lib (1.3-3) ...
200s Setting up python3-biopython (1.81+dfsg-3) ...
201s Setting up python3-cgecore (1.5.6+ds-1) ...
202s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
202s   start = re.search("^-*(\w+)", align_query).start(1)
202s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
202s   end = re.search("\w+(-*)$", align_query).start(1)
202s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
202s   """
202s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
202s   src = re.sub('[^\w/\-\.\*]', '', src)
202s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
202s   dst = re.sub('[^\w/\-\.\*]', '', dst)
202s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
202s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
202s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
202s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
202s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
202s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
202s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
202s   src = re.sub('[^\w/\-\.\*]', '', src)
202s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
202s   dst = re.sub('[^\w/\-\.\*]', '', dst)
202s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
202s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
202s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
202s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
202s Setting up virulencefinder (2.0.5-1ubuntu1) ...
202s Setting up autopkgtest-satdep (0) ...
205s (Reading database ... 55747 files and directories currently installed.)
205s Removing autopkgtest-satdep (0) ...
205s autopkgtest [22:34:22]: test run-unit-test: [-----------------------
206s TEST SUCCEEDED
206s autopkgtest [22:34:23]: test run-unit-test: -----------------------]
207s autopkgtest [22:34:24]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
207s run-unit-test        PASS
207s autopkgtest [22:34:24]: @@@@@@@@@@@@@@@@@@@@ summary
207s run-unit-test        PASS
218s Creating nova instance adt-noble-s390x-virulencefinder-20240317-223057-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240316.img (UUID 7afe023c-7cb8-41b6-91a7-c69e7d1e7c0d)...