0s autopkgtest [02:09:29]: starting date and time: 2024-03-18 02:09:29+0000
  0s autopkgtest [02:09:29]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [02:09:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.t7_tj7h3/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@bos03-arm64-21.secgroup --name adt-noble-arm64-virulencefinder-20240318-020929-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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://ftpmaster.internal/ubuntu/
133s autopkgtest [02:11:42]: testbed dpkg architecture: arm64
133s autopkgtest [02:11:42]: testbed apt version: 2.7.12
133s autopkgtest [02:11:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup
133s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
134s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
134s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
134s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
134s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB]
134s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB]
134s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
134s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
134s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
134s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB]
134s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
134s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB]
134s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
136s Fetched 9189 kB in 2s (5495 kB/s)
136s Reading package lists...
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Calculating upgrade...
140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
140s Reading package lists...
140s Building dependency tree...
140s Reading state information...
141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
142s sh: Attempting to set up Debian/Ubuntu apt sources automatically
142s sh: Distribution appears to be Ubuntu
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
143s eatmydata is already the newest version (131-1).
143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
143s Reading package lists...
143s Building dependency tree...
143s Reading state information...
144s dbus is already the newest version (1.14.10-4ubuntu1).
144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
145s rng-tools-debian is already the newest version (2.4).
145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s Reading package lists...
145s Building dependency tree...
145s Reading state information...
145s The following packages will be REMOVED:
145s   cloud-init* python3-configobj* python3-debconf*
146s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
146s After this operation, 3252 kB disk space will be freed.
146s (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 ... 74758 files and directories currently installed.)
146s Removing cloud-init (24.1.1-0ubuntu1) ...
147s Removing python3-configobj (5.0.8-3) ...
147s Removing python3-debconf (1.5.86) ...
147s Processing triggers for man-db (2.12.0-3) ...
148s (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 ... 74369 files and directories currently installed.)
148s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ...
148s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
148s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
148s invoke-rc.d: policy-rc.d denied execution of try-restart.
148s Reading package lists...
149s Building dependency tree...
149s Reading state information...
150s linux-generic is already the newest version (6.8.0-11.11+1).
150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
150s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
150s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
151s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
152s Reading package lists...
153s Reading package lists...
153s Building dependency tree...
153s Reading state information...
153s Calculating upgrade...
154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
154s Reading package lists...
154s Building dependency tree...
154s Reading state information...
154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
155s autopkgtest [02:12:04]: rebooting testbed after setup commands that affected boot
182s autopkgtest [02:12:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
185s autopkgtest [02:12:34]: @@@@@@@@@@@@@@@@@@@@ apt-source virulencefinder
188s Get:1 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (dsc) [2273 B]
188s Get:2 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (tar) [264 kB]
188s Get:3 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (diff) [6148 B]
189s gpgv: Signature made Sat Mar  9 11:28:05 2024 UTC
189s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
189s gpgv: Can't check signature: No public key
189s dpkg-source: warning: cannot verify inline signature for ./virulencefinder_2.0.5-1ubuntu1.dsc: no acceptable signature found
189s autopkgtest [02:12:38]: testing package virulencefinder version 2.0.5-1ubuntu1
189s autopkgtest [02:12:38]: build not needed
190s autopkgtest [02:12:39]: test run-unit-test: preparing testbed
191s Reading package lists...
191s Building dependency tree...
191s Reading state information...
192s Starting pkgProblemResolver with broken count: 0
192s Starting 2 pkgProblemResolver with broken count: 0
192s Done
192s The following additional packages will be installed:
192s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
192s   fonts-urw-base35 kma libblas3 libcairo2 libdeflate0 libfontconfig1
192s   libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
192s   libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2
192s   liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libopenjp2-7
192s   libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib libraqm0
192s   libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0
192s   libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data python3-biopython
192s   python3-cairo python3-cgecore python3-freetype python3-numpy python3-pil
192s   python3-reportlab python3-rlpycairo python3-tabulate python3.11
192s   python3.11-minimal sgml-base virulencefinder virulencefinder-examples
192s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
192s Suggested packages:
192s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils
192s   python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3
192s   phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf
192s   python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise
192s   gcc gfortran python3-dev python3-pytest python-pil-doc pdf-viewer
192s   python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm
192s   python3.11-venv python3.11-doc binfmt-support sgml-base-doc debhelper
192s Recommended packages:
192s   python-biopython-doc python3-olefile
192s The following NEW packages will be installed:
192s   autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra
192s   fonts-dejavu-mono fonts-urw-base35 kma libblas3 libcairo2 libdeflate0
192s   libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3
192s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3
192s   liblcms2-2 liblerc4 libmbedcrypto7 libmbedtls14 libmbedx509-1 libopenjp2-7
192s   libpixman-1-0 libpython3.11-minimal libpython3.11-stdlib libraqm0
192s   libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0
192s   libxcb-shm0 libxrender1 ncbi-blast+ ncbi-data python3-biopython
192s   python3-cairo python3-cgecore python3-freetype python3-numpy python3-pil
192s   python3-reportlab python3-rlpycairo python3-tabulate python3.11
192s   python3.11-minimal sgml-base virulencefinder virulencefinder-examples
192s   w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
192s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded.
192s Need to get 51.6 MB/51.6 MB of archives.
192s After this operation, 197 MB of additional disk space will be used.
192s Get:1 /tmp/autopkgtest.kYY5Q2/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B]
192s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
193s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
193s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB]
193s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
193s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
193s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
193s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
193s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB]
193s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
193s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
193s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB]
193s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
193s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
193s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB]
193s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 kma arm64 1.4.14-2 [223 kB]
193s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
193s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
193s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
193s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
193s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
193s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
193s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
193s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
193s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
193s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
193s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
193s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
193s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
193s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
193s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
193s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
193s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
193s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
193s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB]
193s Get:36 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB]
193s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB]
193s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
193s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
193s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
194s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
194s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
194s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
194s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
194s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
194s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB]
194s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
194s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
194s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
194s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB]
194s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB]
194s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
194s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB]
194s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB]
194s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
194s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB]
194s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cgecore all 1.5.6+ds-1 [28.8 kB]
194s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB]
194s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 virulencefinder all 2.0.5-1ubuntu1 [13.7 kB]
194s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 virulencefinder-examples all 2.0.5-1ubuntu1 [373 kB]
195s Fetched 51.6 MB in 2s (27.5 MB/s)
195s Selecting previously unselected package libpython3.11-minimal:arm64.
195s (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 ... 74314 files and directories currently installed.)
195s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ...
195s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
195s Selecting previously unselected package python3.11-minimal.
195s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ...
195s Unpacking python3.11-minimal (3.11.8-1) ...
195s Selecting previously unselected package sgml-base.
195s Preparing to unpack .../02-sgml-base_1.31_all.deb ...
195s Unpacking sgml-base (1.31) ...
195s Selecting previously unselected package libpython3.11-stdlib:arm64.
195s Preparing to unpack .../03-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
195s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
195s Selecting previously unselected package python3.11.
195s Preparing to unpack .../04-python3.11_3.11.8-1_arm64.deb ...
195s Unpacking python3.11 (3.11.8-1) ...
195s Selecting previously unselected package fonts-dejavu-mono.
195s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ...
195s Unpacking fonts-dejavu-mono (2.37-8) ...
195s Selecting previously unselected package fonts-dejavu-core.
195s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ...
195s Unpacking fonts-dejavu-core (2.37-8) ...
195s Selecting previously unselected package libfontenc1:arm64.
195s Preparing to unpack .../07-libfontenc1_1%3a1.1.8-1_arm64.deb ...
195s Unpacking libfontenc1:arm64 (1:1.1.8-1) ...
195s Selecting previously unselected package x11-common.
195s Preparing to unpack .../08-x11-common_1%3a7.7+23ubuntu2_all.deb ...
195s Unpacking x11-common (1:7.7+23ubuntu2) ...
195s Selecting previously unselected package xfonts-encodings.
195s Preparing to unpack .../09-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
195s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
195s Selecting previously unselected package xfonts-utils.
195s Preparing to unpack .../10-xfonts-utils_1%3a7.7+6build2_arm64.deb ...
195s Unpacking xfonts-utils (1:7.7+6build2) ...
195s Selecting previously unselected package fonts-urw-base35.
195s Preparing to unpack .../11-fonts-urw-base35_20200910-8_all.deb ...
195s Unpacking fonts-urw-base35 (20200910-8) ...
196s Selecting previously unselected package fontconfig-config.
196s Preparing to unpack .../12-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
196s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
196s Selecting previously unselected package fonts-dejavu-extra.
196s Preparing to unpack .../13-fonts-dejavu-extra_2.37-8_all.deb ...
196s Unpacking fonts-dejavu-extra (2.37-8) ...
196s Selecting previously unselected package kma.
196s Preparing to unpack .../14-kma_1.4.14-2_arm64.deb ...
196s Unpacking kma (1.4.14-2) ...
196s Selecting previously unselected package libblas3:arm64.
196s Preparing to unpack .../15-libblas3_3.12.0-3_arm64.deb ...
196s Unpacking libblas3:arm64 (3.12.0-3) ...
196s Selecting previously unselected package libfontconfig1:arm64.
196s Preparing to unpack .../16-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
196s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
196s Selecting previously unselected package libpixman-1-0:arm64.
196s Preparing to unpack .../17-libpixman-1-0_0.42.2-1_arm64.deb ...
196s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
196s Selecting previously unselected package libxcb-render0:arm64.
196s Preparing to unpack .../18-libxcb-render0_1.15-1_arm64.deb ...
196s Unpacking libxcb-render0:arm64 (1.15-1) ...
196s Selecting previously unselected package libxcb-shm0:arm64.
196s Preparing to unpack .../19-libxcb-shm0_1.15-1_arm64.deb ...
196s Unpacking libxcb-shm0:arm64 (1.15-1) ...
196s Selecting previously unselected package libxrender1:arm64.
196s Preparing to unpack .../20-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
196s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
196s Selecting previously unselected package libcairo2:arm64.
196s Preparing to unpack .../21-libcairo2_1.18.0-1_arm64.deb ...
196s Unpacking libcairo2:arm64 (1.18.0-1) ...
196s Selecting previously unselected package libdeflate0:arm64.
196s Preparing to unpack .../22-libdeflate0_1.19-1_arm64.deb ...
196s Unpacking libdeflate0:arm64 (1.19-1) ...
196s Selecting previously unselected package libgfortran5:arm64.
196s Preparing to unpack .../23-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
196s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
196s Selecting previously unselected package libgomp1:arm64.
196s Preparing to unpack .../24-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
196s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
196s Selecting previously unselected package libgraphite2-3:arm64.
196s Preparing to unpack .../25-libgraphite2-3_1.3.14-2_arm64.deb ...
196s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
196s Selecting previously unselected package libharfbuzz0b:arm64.
196s Preparing to unpack .../26-libharfbuzz0b_8.3.0-2_arm64.deb ...
196s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
196s Selecting previously unselected package libimagequant0:arm64.
196s Preparing to unpack .../27-libimagequant0_2.18.0-1_arm64.deb ...
196s Unpacking libimagequant0:arm64 (2.18.0-1) ...
196s Selecting previously unselected package libjpeg-turbo8:arm64.
196s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
196s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
196s Selecting previously unselected package libjpeg8:arm64.
196s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_arm64.deb ...
196s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
196s Selecting previously unselected package liblapack3:arm64.
196s Preparing to unpack .../30-liblapack3_3.12.0-3_arm64.deb ...
196s Unpacking liblapack3:arm64 (3.12.0-3) ...
196s Selecting previously unselected package liblcms2-2:arm64.
196s Preparing to unpack .../31-liblcms2-2_2.14-2_arm64.deb ...
196s Unpacking liblcms2-2:arm64 (2.14-2) ...
196s Selecting previously unselected package liblerc4:arm64.
196s Preparing to unpack .../32-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
196s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
196s Selecting previously unselected package libmbedcrypto7:arm64.
196s Preparing to unpack .../33-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ...
196s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ...
196s Selecting previously unselected package libmbedx509-1:arm64.
196s Preparing to unpack .../34-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ...
196s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ...
197s Selecting previously unselected package libmbedtls14:arm64.
197s Preparing to unpack .../35-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ...
197s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ...
197s Selecting previously unselected package libraqm0:arm64.
197s Preparing to unpack .../36-libraqm0_0.10.1-1_arm64.deb ...
197s Unpacking libraqm0:arm64 (0.10.1-1) ...
197s Selecting previously unselected package libsharpyuv0:arm64.
197s Preparing to unpack .../37-libsharpyuv0_1.3.2-0.4_arm64.deb ...
197s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
197s Selecting previously unselected package libjbig0:arm64.
197s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
197s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
197s Selecting previously unselected package libwebp7:arm64.
197s Preparing to unpack .../39-libwebp7_1.3.2-0.4_arm64.deb ...
197s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
197s Selecting previously unselected package libtiff6:arm64.
197s Preparing to unpack .../40-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
197s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
197s Selecting previously unselected package libwebpdemux2:arm64.
197s Preparing to unpack .../41-libwebpdemux2_1.3.2-0.4_arm64.deb ...
197s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
197s Selecting previously unselected package libwebpmux3:arm64.
197s Preparing to unpack .../42-libwebpmux3_1.3.2-0.4_arm64.deb ...
197s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
197s Selecting previously unselected package ncbi-data.
197s Preparing to unpack .../43-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
197s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
197s Selecting previously unselected package ncbi-blast+.
197s Preparing to unpack .../44-ncbi-blast+_2.12.0+ds-4_arm64.deb ...
197s Unpacking ncbi-blast+ (2.12.0+ds-4) ...
197s Selecting previously unselected package python3-numpy.
197s Preparing to unpack .../45-python3-numpy_1%3a1.24.2-2_arm64.deb ...
197s Unpacking python3-numpy (1:1.24.2-2) ...
198s Selecting previously unselected package libopenjp2-7:arm64.
198s Preparing to unpack .../46-libopenjp2-7_2.5.0-2_arm64.deb ...
198s Unpacking libopenjp2-7:arm64 (2.5.0-2) ...
198s Selecting previously unselected package python3-pil:arm64.
198s Preparing to unpack .../47-python3-pil_10.2.0-1_arm64.deb ...
198s Unpacking python3-pil:arm64 (10.2.0-1) ...
198s Selecting previously unselected package python3-cairo.
198s Preparing to unpack .../48-python3-cairo_1.25.1-2_arm64.deb ...
198s Unpacking python3-cairo (1.25.1-2) ...
198s Selecting previously unselected package python3-freetype.
198s Preparing to unpack .../49-python3-freetype_2.4.0-1_all.deb ...
198s Unpacking python3-freetype (2.4.0-1) ...
198s Selecting previously unselected package python3-rlpycairo.
198s Preparing to unpack .../50-python3-rlpycairo_0.3.0-3_all.deb ...
198s Unpacking python3-rlpycairo (0.3.0-3) ...
198s Selecting previously unselected package python3-reportlab.
198s Preparing to unpack .../51-python3-reportlab_4.1.0-1_all.deb ...
198s Unpacking python3-reportlab (4.1.0-1) ...
198s Selecting previously unselected package xml-core.
198s Preparing to unpack .../52-xml-core_0.19_all.deb ...
198s Unpacking xml-core (0.19) ...
198s Selecting previously unselected package w3c-sgml-lib.
198s Preparing to unpack .../53-w3c-sgml-lib_1.3-3_all.deb ...
198s Unpacking w3c-sgml-lib (1.3-3) ...
198s Selecting previously unselected package python3-biopython.
198s Preparing to unpack .../54-python3-biopython_1.81+dfsg-3_arm64.deb ...
198s Unpacking python3-biopython (1.81+dfsg-3) ...
198s Selecting previously unselected package python3-cgecore.
198s Preparing to unpack .../55-python3-cgecore_1.5.6+ds-1_all.deb ...
198s Unpacking python3-cgecore (1.5.6+ds-1) ...
198s Selecting previously unselected package python3-tabulate.
198s Preparing to unpack .../56-python3-tabulate_0.8.10-1_all.deb ...
198s Unpacking python3-tabulate (0.8.10-1) ...
198s Selecting previously unselected package virulencefinder.
198s Preparing to unpack .../57-virulencefinder_2.0.5-1ubuntu1_all.deb ...
198s Unpacking virulencefinder (2.0.5-1ubuntu1) ...
198s Selecting previously unselected package virulencefinder-examples.
198s Preparing to unpack .../58-virulencefinder-examples_2.0.5-1ubuntu1_all.deb ...
198s Unpacking virulencefinder-examples (2.0.5-1ubuntu1) ...
198s Selecting previously unselected package autopkgtest-satdep.
198s Preparing to unpack .../59-1-autopkgtest-satdep.deb ...
198s Unpacking autopkgtest-satdep (0) ...
198s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
198s Setting up liblcms2-2:arm64 (2.14-2) ...
198s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
198s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
198s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
198s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
198s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
198s Setting up libxcb-render0:arm64 (1.15-1) ...
198s Setting up x11-common (1:7.7+23ubuntu2) ...
199s Setting up libdeflate0:arm64 (1.19-1) ...
199s Setting up python3-tabulate (0.8.10-1) ...
199s Setting up virulencefinder-examples (2.0.5-1ubuntu1) ...
199s Setting up libxcb-shm0:arm64 (1.15-1) ...
199s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
199s Setting up python3-freetype (2.4.0-1) ...
199s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
199s Setting up libfontenc1:arm64 (1:1.1.8-1) ...
199s Setting up libblas3:arm64 (3.12.0-3) ...
199s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
199s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ...
199s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
199s Setting up libimagequant0:arm64 (2.18.0-1) ...
199s Setting up fonts-dejavu-mono (2.37-8) ...
199s Setting up fonts-dejavu-core (2.37-8) ...
199s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
199s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
199s Setting up libwebp7:arm64 (1.3.2-0.4) ...
199s Setting up fonts-dejavu-extra (2.37-8) ...
199s Setting up kma (1.4.14-2) ...
199s Setting up libopenjp2-7:arm64 (2.5.0-2) ...
199s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
199s Setting up sgml-base (1.31) ...
199s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
199s Setting up libwebpmux3:arm64 (1.3.2-0.4) ...
199s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
199s Setting up python3.11-minimal (3.11.8-1) ...
200s Setting up liblapack3:arm64 (3.12.0-3) ...
200s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
200s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ...
200s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ...
200s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
200s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ...
200s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
200s Setting up xfonts-utils (1:7.7+6build2) ...
200s Setting up ncbi-blast+ (2.12.0+ds-4) ...
200s Setting up libraqm0:arm64 (0.10.1-1) ...
200s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
200s Setting up xml-core (0.19) ...
200s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
200s Setting up python3.11 (3.11.8-1) ...
201s Setting up fonts-urw-base35 (20200910-8) ...
201s Setting up libcairo2:arm64 (1.18.0-1) ...
201s Setting up python3-pil:arm64 (10.2.0-1) ...
202s Setting up python3-numpy (1:1.24.2-2) ...
203s Setting up python3-cairo (1.25.1-2) ...
203s Setting up python3-rlpycairo (0.3.0-3) ...
204s Setting up python3-reportlab (4.1.0-1) ...
204s Processing triggers for libc-bin (2.39-0ubuntu2) ...
204s Processing triggers for systemd (255.2-3ubuntu2) ...
204s Processing triggers for man-db (2.12.0-3) ...
205s Processing triggers for sgml-base (1.31) ...
205s Setting up w3c-sgml-lib (1.3-3) ...
229s Setting up python3-biopython (1.81+dfsg-3) ...
230s Setting up python3-cgecore (1.5.6+ds-1) ...
230s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
230s   start = re.search("^-*(\w+)", align_query).start(1)
230s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
230s   end = re.search("\w+(-*)$", align_query).start(1)
230s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
230s   """
230s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
230s   src = re.sub('[^\w/\-\.\*]', '', src)
230s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
230s   dst = re.sub('[^\w/\-\.\*]', '', dst)
230s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
230s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
230s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
230s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
230s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
230s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
230s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
230s   src = re.sub('[^\w/\-\.\*]', '', src)
230s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
230s   dst = re.sub('[^\w/\-\.\*]', '', dst)
230s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
230s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
230s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
230s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
230s Setting up virulencefinder (2.0.5-1ubuntu1) ...
230s Setting up autopkgtest-satdep (0) ...
234s (Reading database ... 78582 files and directories currently installed.)
234s Removing autopkgtest-satdep (0) ...
235s autopkgtest [02:13:24]: test run-unit-test: [-----------------------
236s TEST SUCCEEDED
237s autopkgtest [02:13:26]: test run-unit-test: -----------------------]
237s autopkgtest [02:13:26]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
237s run-unit-test        PASS
237s autopkgtest [02:13:26]: @@@@@@@@@@@@@@@@@@@@ summary
237s run-unit-test        PASS
248s Creating nova instance adt-noble-arm64-virulencefinder-20240318-020929-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...