0s autopkgtest [21:20:41]: starting date and time: 2024-03-24 21:20:41+0000
  0s autopkgtest [21:20:41]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [21:20:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hr_aos53/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade virulencefinder --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.12.2-0ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-14.secgroup --name adt-noble-i386-virulencefinder-20240324-212041-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-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/
 64s autopkgtest [21:21:45]: testbed dpkg architecture: amd64
 64s autopkgtest [21:21:45]: testbed apt version: 2.7.12
 65s autopkgtest [21:21:46]: test architecture: i386
 65s autopkgtest [21:21:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 65s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 65s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
 65s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [58.0 kB]
 65s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 65s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3983 kB]
 65s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [490 kB]
 65s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [728 kB]
 65s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
 65s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
 65s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
 65s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
 65s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4417 kB]
 65s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1299 kB]
 65s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
 65s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [97.1 kB]
 65s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.7 kB]
 65s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
 68s Fetched 11.8 MB in 1s (8177 kB/s)
 68s Reading package lists...
 70s Reading package lists...
 70s Building dependency tree...
 70s Reading state information...
 70s Calculating upgrade...
 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 70s Reading package lists...
 71s Building dependency tree...
 71s Reading state information...
 71s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded.
 71s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 71s sh: Distribution appears to be Ubuntu
 72s Reading package lists...
 72s Building dependency tree...
 72s Reading state information...
 73s eatmydata is already the newest version (131-1).
 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 73s dbus is already the newest version (1.14.10-4ubuntu1).
 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 73s Reading package lists...
 73s Building dependency tree...
 73s Reading state information...
 74s rng-tools-debian is already the newest version (2.4).
 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 74s Reading package lists...
 74s Building dependency tree...
 74s Reading state information...
 74s The following packages will be REMOVED:
 74s   cloud-init* python3-configobj* python3-debconf*
 74s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
 74s After this operation, 3256 kB disk space will be freed.
 75s (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 ... 71864 files and directories currently installed.)
 75s Removing cloud-init (24.1.2-0ubuntu1) ...
 75s Removing python3-configobj (5.0.8-3) ...
 75s Removing python3-debconf (1.5.86) ...
 75s Processing triggers for man-db (2.12.0-3) ...
 76s (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 ... 71475 files and directories currently installed.)
 76s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
 76s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 76s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
 76s invoke-rc.d: policy-rc.d denied execution of try-restart.
 77s Reading package lists...
 77s Building dependency tree...
 77s Reading state information...
 77s linux-generic is already the newest version (6.8.0-11.11+1).
 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 77s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 77s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 77s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 79s Reading package lists...
 79s Reading package lists...
 79s Building dependency tree...
 79s Reading state information...
 80s Calculating upgrade...
 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 80s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 80s autopkgtest [21:22:01]: rebooting testbed after setup commands that affected boot
124s autopkgtest [21:22:45]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
125s autopkgtest [21:22:46]: @@@@@@@@@@@@@@@@@@@@ apt-source virulencefinder
126s Get:1 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (dsc) [2273 B]
126s Get:2 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (tar) [264 kB]
126s Get:3 http://ftpmaster.internal/ubuntu noble/universe virulencefinder 2.0.5-1ubuntu1 (diff) [6148 B]
126s gpgv: Signature made Sat Mar  9 11:28:05 2024 UTC
126s gpgv:                using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37
126s gpgv: Can't check signature: No public key
126s dpkg-source: warning: cannot verify inline signature for ./virulencefinder_2.0.5-1ubuntu1.dsc: no acceptable signature found
126s autopkgtest [21:22:47]: testing package virulencefinder version 2.0.5-1ubuntu1
126s autopkgtest [21:22:47]: build not needed
126s autopkgtest [21:22:47]: test run-unit-test: preparing testbed
129s Note, using file '/tmp/autopkgtest.J8JcKm/1-autopkgtest-satdep.dsc' to get the build dependencies
129s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s Starting pkgProblemResolver with broken count: 0
130s Starting 2 pkgProblemResolver with broken count: 0
130s Done
130s The following NEW packages will be installed:
130s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
130s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
130s   fonts-urw-base35 g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc
130s   gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu kma libasan8 libatomic1
130s   libblas3 libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdeflate0
130s   libfontconfig1 libfontenc1 libgcc-13-dev libgfortran5 libgomp1
130s   libgraphite2-3 libharfbuzz0b libhwasan0 libimagequant0 libisl23 libitm1
130s   libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 liblerc4 liblsan0
130s   libmbedcrypto7 libmbedtls14 libmbedx509-1 libmpc3 libopenjp2-7 libpixman-1-0
130s   libquadmath0 libraqm0 libsharpyuv0 libstdc++-13-dev libtiff6 libtsan2
130s   libubsan1 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0
130s   libxrender1 linux-libc-dev ncbi-blast+ ncbi-data python3-biopython
130s   python3-cairo python3-cgecore python3-freetype python3-numpy python3-pil
130s   python3-reportlab python3-rlpycairo python3-tabulate rpcsvc-proto sgml-base
130s   virulencefinder virulencefinder-examples w3c-sgml-lib x11-common
130s   xfonts-encodings xfonts-utils xml-core
130s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
130s Need to get 116 MB of archives.
130s After this operation, 434 MB of additional disk space will be used.
130s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 sgml-base all 1.31 [11.4 kB]
130s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB]
130s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
130s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
130s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
130s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB]
130s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
130s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
130s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
130s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
130s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
130s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
130s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
130s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
130s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
130s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
130s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
130s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
130s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
130s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
130s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
130s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
130s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
130s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
131s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
131s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
131s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
131s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
131s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
131s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
131s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
131s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
131s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
131s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
131s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
131s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libfontenc1 amd64 1:1.1.8-1 [14.0 kB]
131s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
131s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
131s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 xfonts-utils amd64 1:7.7+6build2 [94.6 kB]
131s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB]
131s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
131s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-extra all 2.37-8 [1947 kB]
131s Get:43 http://ftpmaster.internal/ubuntu noble/universe amd64 kma amd64 1.4.14-2 [223 kB]
131s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
131s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
131s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
131s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
131s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
131s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
131s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
131s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
131s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
131s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
131s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
131s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libimagequant0 amd64 2.18.0-1 [36.3 kB]
131s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
131s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
131s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
131s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 liblcms2-2 amd64 2.14-2 [161 kB]
131s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
131s Get:61 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedcrypto7 amd64 2.28.7-1ubuntu1 [206 kB]
131s Get:62 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedx509-1 amd64 2.28.7-1ubuntu1 [46.4 kB]
131s Get:63 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedtls14 amd64 2.28.7-1ubuntu1 [82.1 kB]
131s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libraqm0 amd64 0.10.1-1 [14.6 kB]
131s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
131s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
131s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
131s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
131s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libwebpdemux2 amd64 1.3.2-0.4 [12.4 kB]
131s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libwebpmux3 amd64 1.3.2-0.4 [25.6 kB]
131s Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
131s Get:72 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.6 MB]
131s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 python3-numpy amd64 1:1.24.2-2 [7141 kB]
131s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libopenjp2-7 amd64 2.5.0-2 [174 kB]
131s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pil amd64 10.2.0-1 [487 kB]
131s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 python3-cairo amd64 1.25.1-2 [148 kB]
131s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-freetype all 2.4.0-1 [83.1 kB]
131s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B]
131s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-reportlab all 4.1.0-1 [683 kB]
131s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 xml-core all 0.19 [20.3 kB]
131s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB]
131s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-biopython amd64 1.81+dfsg-3 [1670 kB]
131s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 python3-cgecore all 1.5.6+ds-1 [28.8 kB]
131s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 python3-tabulate all 0.8.10-1 [38.2 kB]
131s Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 virulencefinder all 2.0.5-1ubuntu1 [13.7 kB]
131s Get:86 http://ftpmaster.internal/ubuntu noble/universe amd64 virulencefinder-examples all 2.0.5-1ubuntu1 [373 kB]
132s Fetched 116 MB in 1s (103 MB/s)
132s Selecting previously unselected package sgml-base.
132s (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 ... 71420 files and directories currently installed.)
132s Preparing to unpack .../00-sgml-base_1.31_all.deb ...
132s Unpacking sgml-base (1.31) ...
132s Selecting previously unselected package libc-dev-bin.
132s Preparing to unpack .../01-libc-dev-bin_2.39-0ubuntu6_amd64.deb ...
132s Unpacking libc-dev-bin (2.39-0ubuntu6) ...
132s Selecting previously unselected package linux-libc-dev:amd64.
132s Preparing to unpack .../02-linux-libc-dev_6.8.0-11.11_amd64.deb ...
132s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
132s Selecting previously unselected package libcrypt-dev:amd64.
132s Preparing to unpack .../03-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
132s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
132s Selecting previously unselected package rpcsvc-proto.
132s Preparing to unpack .../04-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
132s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
132s Selecting previously unselected package libc6-dev:amd64.
132s Preparing to unpack .../05-libc6-dev_2.39-0ubuntu6_amd64.deb ...
132s Unpacking libc6-dev:amd64 (2.39-0ubuntu6) ...
132s Selecting previously unselected package libisl23:amd64.
132s Preparing to unpack .../06-libisl23_0.26-3_amd64.deb ...
132s Unpacking libisl23:amd64 (0.26-3) ...
132s Selecting previously unselected package libmpc3:amd64.
132s Preparing to unpack .../07-libmpc3_1.3.1-1_amd64.deb ...
132s Unpacking libmpc3:amd64 (1.3.1-1) ...
132s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
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133s Selecting previously unselected package cpp-x86-64-linux-gnu.
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133s Selecting previously unselected package cpp.
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133s Unpacking cpp (4:13.2.0-7ubuntu1) ...
133s Selecting previously unselected package libcc1-0:amd64.
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133s Selecting previously unselected package libgomp1:amd64.
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133s Selecting previously unselected package libitm1:amd64.
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133s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package libatomic1:amd64.
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133s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package libasan8:amd64.
133s Preparing to unpack .../16-libasan8_14-20240303-1ubuntu1_amd64.deb ...
133s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package liblsan0:amd64.
133s Preparing to unpack .../17-liblsan0_14-20240303-1ubuntu1_amd64.deb ...
133s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package libtsan2:amd64.
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133s Selecting previously unselected package libubsan1:amd64.
133s Preparing to unpack .../19-libubsan1_14-20240303-1ubuntu1_amd64.deb ...
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133s Selecting previously unselected package libhwasan0:amd64.
133s Preparing to unpack .../20-libhwasan0_14-20240303-1ubuntu1_amd64.deb ...
133s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package libquadmath0:amd64.
133s Preparing to unpack .../21-libquadmath0_14-20240303-1ubuntu1_amd64.deb ...
133s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ...
133s Selecting previously unselected package libgcc-13-dev:amd64.
133s Preparing to unpack .../22-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ...
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133s Selecting previously unselected package gcc-13-x86-64-linux-gnu.
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134s Selecting previously unselected package gcc-13.
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134s Selecting previously unselected package gcc-x86-64-linux-gnu.
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134s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
134s Selecting previously unselected package gcc.
134s Preparing to unpack .../26-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
134s Unpacking gcc (4:13.2.0-7ubuntu1) ...
134s Selecting previously unselected package libstdc++-13-dev:amd64.
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134s Selecting previously unselected package g++-13-x86-64-linux-gnu.
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134s Selecting previously unselected package g++-13.
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134s Unpacking g++-13 (13.2.0-17ubuntu2) ...
134s Selecting previously unselected package g++-x86-64-linux-gnu.
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134s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
134s Selecting previously unselected package g++.
134s Preparing to unpack .../31-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
134s Unpacking g++ (4:13.2.0-7ubuntu1) ...
134s Selecting previously unselected package build-essential.
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134s Selecting previously unselected package fonts-dejavu-mono.
134s Preparing to unpack .../33-fonts-dejavu-mono_2.37-8_all.deb ...
134s Unpacking fonts-dejavu-mono (2.37-8) ...
134s Selecting previously unselected package fonts-dejavu-core.
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134s Unpacking fonts-dejavu-core (2.37-8) ...
135s Selecting previously unselected package libfontenc1:amd64.
135s Preparing to unpack .../35-libfontenc1_1%3a1.1.8-1_amd64.deb ...
135s Unpacking libfontenc1:amd64 (1:1.1.8-1) ...
135s Selecting previously unselected package x11-common.
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135s Selecting previously unselected package xfonts-encodings.
135s Preparing to unpack .../37-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
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135s Selecting previously unselected package xfonts-utils.
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135s Selecting previously unselected package fonts-urw-base35.
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135s Selecting previously unselected package fontconfig-config.
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135s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
135s Selecting previously unselected package fonts-dejavu-extra.
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135s Unpacking fonts-dejavu-extra (2.37-8) ...
135s Selecting previously unselected package kma.
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135s Selecting previously unselected package libblas3:amd64.
135s Preparing to unpack .../43-libblas3_3.12.0-3_amd64.deb ...
135s Unpacking libblas3:amd64 (3.12.0-3) ...
135s Selecting previously unselected package libfontconfig1:amd64.
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135s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
135s Selecting previously unselected package libpixman-1-0:amd64.
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135s Selecting previously unselected package libxcb-render0:amd64.
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135s Selecting previously unselected package libxcb-shm0:amd64.
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135s Selecting previously unselected package libxrender1:amd64.
135s Preparing to unpack .../48-libxrender1_1%3a0.9.10-1.1_amd64.deb ...
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135s Selecting previously unselected package libcairo2:amd64.
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135s Selecting previously unselected package libdeflate0:amd64.
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135s Selecting previously unselected package libgfortran5:amd64.
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136s Selecting previously unselected package libharfbuzz0b:amd64.
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136s Selecting previously unselected package libimagequant0:amd64.
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136s Selecting previously unselected package libjpeg-turbo8:amd64.
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136s Selecting previously unselected package liblapack3:amd64.
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136s Selecting previously unselected package liblerc4:amd64.
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136s Selecting previously unselected package libmbedcrypto7:amd64.
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136s Selecting previously unselected package libmbedx509-1:amd64.
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136s Selecting previously unselected package libmbedtls14:amd64.
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138s Setting up libgraphite2-3:amd64 (1.3.14-2) ...
138s Setting up liblcms2-2:amd64 (2.14-2) ...
138s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
138s Setting up libpixman-1-0:amd64 (0.42.2-1) ...
138s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ...
138s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
138s Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
138s Setting up libxcb-render0:amd64 (1.15-1) ...
138s Setting up x11-common (1:7.7+23ubuntu2) ...
138s Setting up libdeflate0:amd64 (1.19-1) ...
138s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ...
138s Setting up python3-tabulate (0.8.10-1) ...
138s Setting up virulencefinder-examples (2.0.5-1ubuntu1) ...
138s Setting up libxcb-shm0:amd64 (1.15-1) ...
138s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ...
138s Setting up python3-freetype (2.4.0-1) ...
138s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ...
138s Setting up libfontenc1:amd64 (1:1.1.8-1) ...
138s Setting up libblas3:amd64 (3.12.0-3) ...
138s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
138s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
138s Setting up libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ...
138s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
138s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libimagequant0:amd64 (2.18.0-1) ...
138s Setting up fonts-dejavu-mono (2.37-8) ...
138s Setting up libmpc3:amd64 (1.3.1-1) ...
138s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ...
138s Setting up fonts-dejavu-core (2.37-8) ...
138s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ...
138s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libwebp7:amd64 (1.3.2-0.4) ...
138s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ...
138s Setting up fonts-dejavu-extra (2.37-8) ...
138s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ...
138s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ...
138s Setting up kma (1.4.14-2) ...
138s Setting up libopenjp2-7:amd64 (2.5.0-2) ...
138s Setting up libharfbuzz0b:amd64 (8.3.0-2) ...
138s Setting up sgml-base (1.31) ...
138s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libisl23:amd64 (0.26-3) ...
138s Setting up libc-dev-bin (2.39-0ubuntu6) ...
138s Setting up libwebpmux3:amd64 (1.3.2-0.4) ...
138s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ...
138s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ...
138s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
138s Setting up liblapack3:amd64 (3.12.0-3) ...
138s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
138s Setting up libmbedx509-1:amd64 (2.28.7-1ubuntu1) ...
138s Setting up libmbedtls14:amd64 (2.28.7-1ubuntu1) ...
138s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
138s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
139s Setting up libwebpdemux2:amd64 (1.3.2-0.4) ...
139s Setting up xfonts-utils (1:7.7+6build2) ...
139s Setting up ncbi-blast+ (2.12.0+ds-4) ...
139s Setting up libraqm0:amd64 (0.10.1-1) ...
139s Setting up python3-numpy (1:1.24.2-2) ...
140s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
140s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
140s Setting up xml-core (0.19) ...
140s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ...
140s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
140s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
140s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
140s Setting up cpp-13 (13.2.0-17ubuntu2) ...
140s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
140s Setting up fonts-urw-base35 (20200910-8) ...
141s Setting up libcairo2:amd64 (1.18.0-1) ...
141s Setting up python3-pil:amd64 (10.2.0-1) ...
141s Setting up gcc-13 (13.2.0-17ubuntu2) ...
141s Setting up cpp (4:13.2.0-7ubuntu1) ...
141s Setting up python3-cairo (1.25.1-2) ...
141s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
141s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
141s Setting up gcc (4:13.2.0-7ubuntu1) ...
141s Setting up python3-rlpycairo (0.3.0-3) ...
141s Setting up python3-reportlab (4.1.0-1) ...
142s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
142s Setting up g++-13 (13.2.0-17ubuntu2) ...
142s Setting up g++ (4:13.2.0-7ubuntu1) ...
142s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
142s Setting up build-essential (12.10ubuntu1) ...
142s Processing triggers for libc-bin (2.39-0ubuntu6) ...
142s Processing triggers for man-db (2.12.0-3) ...
143s Processing triggers for sgml-base (1.31) ...
143s Setting up w3c-sgml-lib (1.3-3) ...
169s Setting up python3-biopython (1.81+dfsg-3) ...
170s Setting up python3-cgecore (1.5.6+ds-1) ...
170s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
170s   start = re.search("^-*(\w+)", align_query).start(1)
170s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
170s   end = re.search("\w+(-*)$", align_query).start(1)
170s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
170s   """
170s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
170s   src = re.sub('[^\w/\-\.\*]', '', src)
170s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
170s   dst = re.sub('[^\w/\-\.\*]', '', dst)
170s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
170s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
170s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
170s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
170s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
170s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
170s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
170s   src = re.sub('[^\w/\-\.\*]', '', src)
170s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
170s   dst = re.sub('[^\w/\-\.\*]', '', dst)
170s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
170s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
170s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
170s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
170s Setting up virulencefinder (2.0.5-1ubuntu1) ...
173s Reading package lists...
173s Building dependency tree...
173s Reading state information...
173s Starting pkgProblemResolver with broken count: 0
173s Starting 2 pkgProblemResolver with broken count: 0
173s Done
174s The following NEW packages will be installed:
174s   autopkgtest-satdep
174s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
174s Need to get 0 B/696 B of archives.
174s After this operation, 0 B of additional disk space will be used.
174s Get:1 /tmp/autopkgtest.J8JcKm/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
174s Selecting previously unselected package autopkgtest-satdep.
174s (Reading database ... 
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(Reading database ... 77874 files and directories currently installed.)
174s Preparing to unpack .../2-autopkgtest-satdep.deb ...
174s Unpacking autopkgtest-satdep (0) ...
174s Setting up autopkgtest-satdep (0) ...
176s (Reading database ... 77874 files and directories currently installed.)
176s Removing autopkgtest-satdep (0) ...
176s autopkgtest [21:23:37]: test run-unit-test: [-----------------------
177s TEST SUCCEEDED
177s autopkgtest [21:23:38]: test run-unit-test: -----------------------]
178s autopkgtest [21:23:39]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
178s run-unit-test        PASS
178s autopkgtest [21:23:39]: @@@@@@@@@@@@@@@@@@@@ summary
178s run-unit-test        PASS
188s Creating nova instance adt-noble-i386-virulencefinder-20240324-212041-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240324.img (UUID 4e56ccec-954f-4884-8b9c-3e1a29e50308)...