0s autopkgtest [02:09:12]: starting date: 2024-03-18
  0s autopkgtest [02:09:12]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt
  0s autopkgtest [02:09:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1adyc88v/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 resfinder --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@bos03-arm64-20.secgroup --name adt-noble-arm64-resfinder-20240318-020912-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/
 87s autopkgtest [02:10:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 88s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 88s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 88s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
 88s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
 88s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB]
 89s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB]
 89s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 89s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
 89s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 89s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB]
 89s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 89s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB]
 89s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 90s Fetched 9189 kB in 2s (5528 kB/s)
 90s Reading package lists...
 93s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 94s Calculating upgrade...
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 94s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 96s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 96s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 96s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 97s Reading package lists...
 97s Reading package lists...
 97s Building dependency tree...
 97s Reading state information...
 98s Calculating upgrade...
 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 98s Reading package lists...
 99s Building dependency tree...
 99s Reading state information...
 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
100s autopkgtest [02:10:52]: testbed dpkg architecture: arm64
107s autopkgtest [02:10:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
108s autopkgtest [02:11:00]: @@@@@@@@@@@@@@@@@@@@ apt-source resfinder
110s Get:1 http://ftpmaster.internal/ubuntu noble/universe resfinder 4.4.2-1 (dsc) [2539 B]
110s Get:2 http://ftpmaster.internal/ubuntu noble/universe resfinder 4.4.2-1 (tar) [89.1 kB]
110s Get:3 http://ftpmaster.internal/ubuntu noble/universe resfinder 4.4.2-1 (tar) [359 kB]
110s Get:4 http://ftpmaster.internal/ubuntu noble/universe resfinder 4.4.2-1 (diff) [8332 B]
110s gpgv: Signature made Tue Jan 16 07:05:55 2024 UTC
110s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
110s gpgv:                issuer "tille@debian.org"
110s gpgv: Can't check signature: No public key
110s dpkg-source: warning: cannot verify inline signature for ./resfinder_4.4.2-1.dsc: no acceptable signature found
110s autopkgtest [02:11:02]: testing package resfinder version 4.4.2-1
110s autopkgtest [02:11:02]: build not needed
111s autopkgtest [02:11:03]: test run-unit-test: preparing testbed
113s Reading package lists...
114s Building dependency tree...
114s Reading state information...
114s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
114s Starting 2 pkgProblemResolver with broken count: 0
114s Done
114s  Done
115s Starting pkgProblemResolver with broken count: 0
115s Starting 2 pkgProblemResolver with broken count: 0
115s Done
115s The following additional packages will be installed:
115s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
115s   fonts-urw-base35 git git-man kma libblas3 libcairo2 libdeflate0
115s   liberror-perl libfontconfig1 libfontenc1 libgfortran5 libgomp1
115s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
115s   liblapack3 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64
115s   libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal
115s   libpython3.11-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
115s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+
115s   ncbi-blast+-legacy ncbi-data python3-biopython python3-cairo python3-cgecore
115s   python3-cgelib python3-dateutil python3-freetype python3-git python3-gitdb
115s   python3-numpy python3-pandas python3-pandas-lib python3-pil
115s   python3-reportlab python3-rlpycairo python3-smmap python3-tabulate
115s   python3.11 python3.11-minimal resfinder resfinder-db resfinder-example
115s   sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
115s Suggested packages:
115s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre git-daemon-run
115s   | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs
115s   git-mediawiki git-svn liblcms2-utils python3-tk bwa clustalo clustalw
115s   dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons
115s   python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib
115s   python3-psycopg2 python3-scipy raxml samtools t-coffee wise python-git-doc
115s   gcc gfortran python3-dev python3-pytest python-pandas-doc
115s   python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools
115s   python-reportlab-doc rl-accel rl-renderpm python3.11-venv python3.11-doc
115s   binfmt-support sgml-base-doc debhelper
115s Recommended packages:
115s   python-biopython-doc python3-scipy python3-matplotlib python3-bottleneck
115s   python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib
115s   python3-lxml python3-tables python3-olefile
115s The following NEW packages will be installed:
115s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
115s   fonts-urw-base35 git git-man kma libblas3 libcairo2 libdeflate0
115s   liberror-perl libfontconfig1 libfontenc1 libgfortran5 libgomp1
115s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
115s   liblapack3 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64
115s   libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal
115s   libpython3.11-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
115s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+
115s   ncbi-blast+-legacy ncbi-data python3-biopython python3-cairo python3-cgecore
115s   python3-cgelib python3-dateutil python3-freetype python3-git python3-gitdb
115s   python3-numpy python3-pandas python3-pandas-lib python3-pil
115s   python3-reportlab python3-rlpycairo python3-smmap python3-tabulate
115s   python3.11 python3.11-minimal resfinder resfinder-db resfinder-example
115s   sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
116s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded.
116s 1 not fully installed or removed.
116s Need to get 79.1 MB of archives.
116s After this operation, 381 MB of additional disk space will be used.
116s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder-db all 0.0+git20220524.fa32d9a-1 [11.3 MB]
116s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
116s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
116s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
116s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
117s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
117s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
117s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
117s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
117s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
117s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
117s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
117s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
117s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
117s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
117s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
117s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
117s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
117s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
117s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
117s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
117s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
117s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
117s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
117s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
117s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
117s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
117s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
117s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
117s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB]
117s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
117s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
117s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB]
117s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
117s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
117s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
117s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
117s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
117s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
117s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
117s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
117s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB]
117s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB]
117s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
117s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB]
117s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB]
117s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB]
117s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB]
117s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
117s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB]
117s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cgecore all 1.5.6+ds-1 [28.8 kB]
117s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB]
117s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
118s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB]
118s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB]
118s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB]
118s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB]
118s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+-legacy all 2.12.0+ds-4build1 [4990 B]
118s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 kma arm64 1.4.14-2 [223 kB]
118s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liberror-perl all 0.17029-2 [25.6 kB]
118s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 git-man all 1:2.43.0-1ubuntu1 [1100 kB]
118s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 git arm64 1:2.43.0-1ubuntu1 [3786 kB]
118s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-smmap all 6.0.0-1 [20.5 kB]
118s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-gitdb all 4.0.11-1 [46.2 kB]
118s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-git all 3.1.37-3 [138 kB]
118s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB]
118s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB]
118s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB]
118s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cgelib all 0.7.3-3 [48.2 kB]
118s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder all 4.4.2-1 [66.5 kB]
118s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder-example all 4.4.2-1 [572 kB]
119s Fetched 79.1 MB in 3s (28.6 MB/s)
119s Selecting previously unselected package resfinder-db.
119s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74758 files and directories currently installed.)
119s Preparing to unpack .../00-resfinder-db_0.0+git20220524.fa32d9a-1_all.deb ...
119s Unpacking resfinder-db (0.0+git20220524.fa32d9a-1) ...
119s Selecting previously unselected package libpython3.11-minimal:arm64.
119s Preparing to unpack .../01-libpython3.11-minimal_3.11.8-1_arm64.deb ...
119s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
119s Selecting previously unselected package python3.11-minimal.
119s Preparing to unpack .../02-python3.11-minimal_3.11.8-1_arm64.deb ...
119s Unpacking python3.11-minimal (3.11.8-1) ...
119s Selecting previously unselected package libpython3.11-stdlib:arm64.
119s Preparing to unpack .../03-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
119s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
119s Selecting previously unselected package python3.11.
120s Preparing to unpack .../04-python3.11_3.11.8-1_arm64.deb ...
120s Unpacking python3.11 (3.11.8-1) ...
120s Selecting previously unselected package libblas3:arm64.
120s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ...
120s Unpacking libblas3:arm64 (3.12.0-3) ...
120s Selecting previously unselected package libgfortran5:arm64.
120s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
120s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
120s Selecting previously unselected package liblapack3:arm64.
120s Preparing to unpack .../07-liblapack3_3.12.0-3_arm64.deb ...
120s Unpacking liblapack3:arm64 (3.12.0-3) ...
120s Selecting previously unselected package python3-numpy.
120s Preparing to unpack .../08-python3-numpy_1%3a1.24.2-2_arm64.deb ...
120s Unpacking python3-numpy (1:1.24.2-2) ...
120s Selecting previously unselected package libgomp1:arm64.
120s Preparing to unpack .../09-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
120s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
120s Selecting previously unselected package libimagequant0:arm64.
120s Preparing to unpack .../10-libimagequant0_2.18.0-1_arm64.deb ...
120s Unpacking libimagequant0:arm64 (2.18.0-1) ...
120s Selecting previously unselected package libjpeg-turbo8:arm64.
120s Preparing to unpack .../11-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
120s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
120s Selecting previously unselected package libjpeg8:arm64.
120s Preparing to unpack .../12-libjpeg8_8c-2ubuntu11_arm64.deb ...
120s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
120s Selecting previously unselected package liblcms2-2:arm64.
120s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ...
120s Unpacking liblcms2-2:arm64 (2.14-2) ...
120s Selecting previously unselected package libopenjp2-7:arm64.
120s Preparing to unpack .../14-libopenjp2-7_2.5.0-2_arm64.deb ...
120s Unpacking libopenjp2-7:arm64 (2.5.0-2) ...
120s Selecting previously unselected package libgraphite2-3:arm64.
120s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_arm64.deb ...
120s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
120s Selecting previously unselected package libharfbuzz0b:arm64.
120s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_arm64.deb ...
120s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
120s Selecting previously unselected package libraqm0:arm64.
120s Preparing to unpack .../17-libraqm0_0.10.1-1_arm64.deb ...
120s Unpacking libraqm0:arm64 (0.10.1-1) ...
120s Selecting previously unselected package libdeflate0:arm64.
120s Preparing to unpack .../18-libdeflate0_1.19-1_arm64.deb ...
120s Unpacking libdeflate0:arm64 (1.19-1) ...
120s Selecting previously unselected package libjbig0:arm64.
120s Preparing to unpack .../19-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
120s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
120s Selecting previously unselected package liblerc4:arm64.
120s Preparing to unpack .../20-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
120s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
120s Selecting previously unselected package libsharpyuv0:arm64.
120s Preparing to unpack .../21-libsharpyuv0_1.3.2-0.4_arm64.deb ...
120s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
120s Selecting previously unselected package libwebp7:arm64.
120s Preparing to unpack .../22-libwebp7_1.3.2-0.4_arm64.deb ...
120s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
120s Selecting previously unselected package libtiff6:arm64.
120s Preparing to unpack .../23-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
120s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
120s Selecting previously unselected package libwebpdemux2:arm64.
120s Preparing to unpack .../24-libwebpdemux2_1.3.2-0.4_arm64.deb ...
120s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
120s Selecting previously unselected package libwebpmux3:arm64.
120s Preparing to unpack .../25-libwebpmux3_1.3.2-0.4_arm64.deb ...
120s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
120s Selecting previously unselected package python3-pil:arm64.
120s Preparing to unpack .../26-python3-pil_10.2.0-1_arm64.deb ...
120s Unpacking python3-pil:arm64 (10.2.0-1) ...
120s Selecting previously unselected package fonts-dejavu-mono.
120s Preparing to unpack .../27-fonts-dejavu-mono_2.37-8_all.deb ...
120s Unpacking fonts-dejavu-mono (2.37-8) ...
121s Selecting previously unselected package fonts-dejavu-core.
121s Preparing to unpack .../28-fonts-dejavu-core_2.37-8_all.deb ...
121s Unpacking fonts-dejavu-core (2.37-8) ...
121s Selecting previously unselected package libfontenc1:arm64.
121s Preparing to unpack .../29-libfontenc1_1%3a1.1.8-1_arm64.deb ...
121s Unpacking libfontenc1:arm64 (1:1.1.8-1) ...
121s Selecting previously unselected package x11-common.
121s Preparing to unpack .../30-x11-common_1%3a7.7+23ubuntu2_all.deb ...
121s Unpacking x11-common (1:7.7+23ubuntu2) ...
121s Selecting previously unselected package xfonts-encodings.
121s Preparing to unpack .../31-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
121s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
121s Selecting previously unselected package xfonts-utils.
121s Preparing to unpack .../32-xfonts-utils_1%3a7.7+6build2_arm64.deb ...
121s Unpacking xfonts-utils (1:7.7+6build2) ...
121s Selecting previously unselected package fonts-urw-base35.
121s Preparing to unpack .../33-fonts-urw-base35_20200910-8_all.deb ...
121s Unpacking fonts-urw-base35 (20200910-8) ...
122s Selecting previously unselected package fontconfig-config.
122s Preparing to unpack .../34-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
122s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
122s Selecting previously unselected package libfontconfig1:arm64.
122s Preparing to unpack .../35-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
122s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
122s Selecting previously unselected package libpixman-1-0:arm64.
122s Preparing to unpack .../36-libpixman-1-0_0.42.2-1_arm64.deb ...
122s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
122s Selecting previously unselected package libxcb-render0:arm64.
122s Preparing to unpack .../37-libxcb-render0_1.15-1_arm64.deb ...
122s Unpacking libxcb-render0:arm64 (1.15-1) ...
122s Selecting previously unselected package libxcb-shm0:arm64.
122s Preparing to unpack .../38-libxcb-shm0_1.15-1_arm64.deb ...
122s Unpacking libxcb-shm0:arm64 (1.15-1) ...
122s Selecting previously unselected package libxrender1:arm64.
122s Preparing to unpack .../39-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
122s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
122s Selecting previously unselected package libcairo2:arm64.
122s Preparing to unpack .../40-libcairo2_1.18.0-1_arm64.deb ...
122s Unpacking libcairo2:arm64 (1.18.0-1) ...
122s Selecting previously unselected package python3-cairo.
122s Preparing to unpack .../41-python3-cairo_1.25.1-2_arm64.deb ...
122s Unpacking python3-cairo (1.25.1-2) ...
122s Selecting previously unselected package python3-freetype.
122s Preparing to unpack .../42-python3-freetype_2.4.0-1_all.deb ...
122s Unpacking python3-freetype (2.4.0-1) ...
122s Selecting previously unselected package python3-rlpycairo.
122s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ...
122s Unpacking python3-rlpycairo (0.3.0-3) ...
122s Selecting previously unselected package fonts-dejavu-extra.
122s Preparing to unpack .../44-fonts-dejavu-extra_2.37-8_all.deb ...
122s Unpacking fonts-dejavu-extra (2.37-8) ...
122s Selecting previously unselected package python3-reportlab.
122s Preparing to unpack .../45-python3-reportlab_4.1.0-1_all.deb ...
122s Unpacking python3-reportlab (4.1.0-1) ...
122s Selecting previously unselected package sgml-base.
122s Preparing to unpack .../46-sgml-base_1.31_all.deb ...
122s Unpacking sgml-base (1.31) ...
122s Selecting previously unselected package xml-core.
122s Preparing to unpack .../47-xml-core_0.19_all.deb ...
122s Unpacking xml-core (0.19) ...
122s Selecting previously unselected package w3c-sgml-lib.
122s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ...
122s Unpacking w3c-sgml-lib (1.3-3) ...
122s Selecting previously unselected package python3-biopython.
122s Preparing to unpack .../49-python3-biopython_1.81+dfsg-3_arm64.deb ...
122s Unpacking python3-biopython (1.81+dfsg-3) ...
123s Selecting previously unselected package python3-cgecore.
123s Preparing to unpack .../50-python3-cgecore_1.5.6+ds-1_all.deb ...
123s Unpacking python3-cgecore (1.5.6+ds-1) ...
123s Selecting previously unselected package python3-tabulate.
123s Preparing to unpack .../51-python3-tabulate_0.8.10-1_all.deb ...
123s Unpacking python3-tabulate (0.8.10-1) ...
123s Selecting previously unselected package ncbi-data.
123s Preparing to unpack .../52-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
123s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
123s Selecting previously unselected package libmbedcrypto7t64:arm64.
123s Preparing to unpack .../53-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ...
123s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ...
123s Selecting previously unselected package libmbedx509-1t64:arm64.
123s Preparing to unpack .../54-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ...
123s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ...
123s Selecting previously unselected package libmbedtls14t64:arm64.
123s Preparing to unpack .../55-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ...
123s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
123s Selecting previously unselected package ncbi-blast+.
123s Preparing to unpack .../56-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ...
123s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ...
124s Selecting previously unselected package ncbi-blast+-legacy.
124s Preparing to unpack .../57-ncbi-blast+-legacy_2.12.0+ds-4build1_all.deb ...
124s Unpacking ncbi-blast+-legacy (2.12.0+ds-4build1) ...
124s Selecting previously unselected package kma.
124s Preparing to unpack .../58-kma_1.4.14-2_arm64.deb ...
124s Unpacking kma (1.4.14-2) ...
124s Selecting previously unselected package liberror-perl.
124s Preparing to unpack .../59-liberror-perl_0.17029-2_all.deb ...
124s Unpacking liberror-perl (0.17029-2) ...
124s Selecting previously unselected package git-man.
124s Preparing to unpack .../60-git-man_1%3a2.43.0-1ubuntu1_all.deb ...
124s Unpacking git-man (1:2.43.0-1ubuntu1) ...
124s Selecting previously unselected package git.
124s Preparing to unpack .../61-git_1%3a2.43.0-1ubuntu1_arm64.deb ...
124s Unpacking git (1:2.43.0-1ubuntu1) ...
124s Selecting previously unselected package python3-smmap.
124s Preparing to unpack .../62-python3-smmap_6.0.0-1_all.deb ...
124s Unpacking python3-smmap (6.0.0-1) ...
124s Selecting previously unselected package python3-gitdb.
124s Preparing to unpack .../63-python3-gitdb_4.0.11-1_all.deb ...
124s Unpacking python3-gitdb (4.0.11-1) ...
124s Selecting previously unselected package python3-git.
124s Preparing to unpack .../64-python3-git_3.1.37-3_all.deb ...
124s Unpacking python3-git (3.1.37-3) ...
124s Selecting previously unselected package python3-dateutil.
124s Preparing to unpack .../65-python3-dateutil_2.8.2-3_all.deb ...
124s Unpacking python3-dateutil (2.8.2-3) ...
124s Selecting previously unselected package python3-pandas-lib:arm64.
124s Preparing to unpack .../66-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ...
124s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
125s Selecting previously unselected package python3-pandas.
125s Preparing to unpack .../67-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ...
125s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ...
125s Selecting previously unselected package python3-cgelib.
125s Preparing to unpack .../68-python3-cgelib_0.7.3-3_all.deb ...
125s Unpacking python3-cgelib (0.7.3-3) ...
125s Selecting previously unselected package resfinder.
125s Preparing to unpack .../69-resfinder_4.4.2-1_all.deb ...
125s Unpacking resfinder (4.4.2-1) ...
125s Selecting previously unselected package resfinder-example.
125s Preparing to unpack .../70-resfinder-example_4.4.2-1_all.deb ...
125s Unpacking resfinder-example (4.4.2-1) ...
125s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
125s Setting up liblcms2-2:arm64 (2.14-2) ...
125s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
125s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
125s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
125s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
125s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ...
125s Setting up resfinder-db (0.0+git20220524.fa32d9a-1) ...
125s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
125s Setting up libxcb-render0:arm64 (1.15-1) ...
125s Setting up x11-common (1:7.7+23ubuntu2) ...
125s Setting up libdeflate0:arm64 (1.19-1) ...
125s Setting up python3-tabulate (0.8.10-1) ...
126s Setting up libxcb-shm0:arm64 (1.15-1) ...
126s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
126s Setting up python3-freetype (2.4.0-1) ...
126s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
126s Setting up liberror-perl (0.17029-2) ...
126s Setting up libfontenc1:arm64 (1:1.1.8-1) ...
126s Setting up libblas3:arm64 (3.12.0-3) ...
126s 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
126s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
126s Setting up libimagequant0:arm64 (2.18.0-1) ...
126s Setting up fonts-dejavu-mono (2.37-8) ...
126s Setting up fonts-dejavu-core (2.37-8) ...
126s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
126s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
126s Setting up libwebp7:arm64 (1.3.2-0.4) ...
126s Setting up fonts-dejavu-extra (2.37-8) ...
126s Setting up kma (1.4.14-2) ...
126s Setting up libopenjp2-7:arm64 (2.5.0-2) ...
126s Setting up git-man (1:2.43.0-1ubuntu1) ...
126s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
126s Setting up python3-dateutil (2.8.2-3) ...
126s Setting up sgml-base (1.31) ...
126s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
126s Setting up resfinder-example (4.4.2-1) ...
126s Setting up libwebpmux3:arm64 (1.3.2-0.4) ...
126s Setting up python3-smmap (6.0.0-1) ...
126s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
126s Setting up python3.11-minimal (3.11.8-1) ...
127s Setting up liblapack3:arm64 (3.12.0-3) ...
127s 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
127s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ...
127s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
127s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ...
127s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
127s Setting up python3-gitdb (4.0.11-1) ...
127s Setting up xfonts-utils (1:7.7+6build2) ...
127s Setting up libraqm0:arm64 (0.10.1-1) ...
127s Setting up git (1:2.43.0-1ubuntu1) ...
127s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
127s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
127s Setting up xml-core (0.19) ...
128s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
128s Setting up python3.11 (3.11.8-1) ...
128s Setting up fonts-urw-base35 (20200910-8) ...
129s Setting up libcairo2:arm64 (1.18.0-1) ...
129s Setting up ncbi-blast+ (2.12.0+ds-4build1) ...
129s Setting up python3-pil:arm64 (10.2.0-1) ...
129s Setting up python3-git (3.1.37-3) ...
129s Setting up python3-numpy (1:1.24.2-2) ...
131s Setting up ncbi-blast+-legacy (2.12.0+ds-4build1) ...
131s Setting up python3-cairo (1.25.1-2) ...
131s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
131s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ...
136s Setting up python3-rlpycairo (0.3.0-3) ...
136s Setting up python3-reportlab (4.1.0-1) ...
136s Setting up python3-cgelib (0.7.3-3) ...
137s Processing triggers for libc-bin (2.39-0ubuntu2) ...
137s Processing triggers for systemd (255.2-3ubuntu2) ...
137s Processing triggers for man-db (2.12.0-3) ...
138s Processing triggers for sgml-base (1.31) ...
138s Setting up w3c-sgml-lib (1.3-3) ...
162s Setting up python3-biopython (1.81+dfsg-3) ...
163s Setting up python3-cgecore (1.5.6+ds-1) ...
163s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
163s   start = re.search("^-*(\w+)", align_query).start(1)
163s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
163s   end = re.search("\w+(-*)$", align_query).start(1)
163s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
163s   """
163s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
163s   src = re.sub('[^\w/\-\.\*]', '', src)
163s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
163s   dst = re.sub('[^\w/\-\.\*]', '', dst)
163s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
163s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
163s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
163s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
163s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
163s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
163s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
163s   src = re.sub('[^\w/\-\.\*]', '', src)
163s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
163s   dst = re.sub('[^\w/\-\.\*]', '', dst)
163s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
163s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
163s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
163s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
163s Setting up resfinder (4.4.2-1) ...
164s Setting up autopkgtest-satdep (0) ...
170s (Reading database ... 82424 files and directories currently installed.)
170s Removing autopkgtest-satdep (0) ...
171s autopkgtest [02:12:03]: test run-unit-test: [-----------------------
172s Indexing files as needed
173s ['INSTALL.py']
174s ['INSTALL.py']
174s Running tests
181s ....
181s ----------------------------------------------------------------------
181s Ran 4 tests in 6.809s
181s 
181s OK
181s Cleanup
181s PASS
181s autopkgtest [02:12:13]: test run-unit-test: -----------------------]
181s run-unit-test        PASS
181s autopkgtest [02:12:13]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
182s autopkgtest [02:12:14]: test version-test: preparing testbed
300s autopkgtest [02:14:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
301s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
301s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB]
302s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
302s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
302s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
302s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB]
302s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
302s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
302s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
302s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB]
303s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
303s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB]
303s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
305s Fetched 9189 kB in 3s (3343 kB/s)
305s Reading package lists...
309s Reading package lists...
310s Building dependency tree...
310s Reading state information...
311s Calculating upgrade...
312s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
312s Reading package lists...
312s Building dependency tree...
312s Reading state information...
313s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
314s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
314s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
314s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
314s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
316s Reading package lists...
316s Reading package lists...
316s Building dependency tree...
316s Reading state information...
316s Calculating upgrade...
317s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
317s Reading package lists...
317s Building dependency tree...
317s Reading state information...
318s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
318s autopkgtest [02:14:30]: testbed dpkg architecture: arm64
321s Reading package lists...
322s Building dependency tree...
322s Reading state information...
322s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
322s Starting 2 pkgProblemResolver with broken count: 0
322s Done
322s  Done
323s Starting pkgProblemResolver with broken count: 0
323s Starting 2 pkgProblemResolver with broken count: 0
323s Done
324s The following additional packages will be installed:
324s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
324s   fonts-urw-base35 git git-man kma libblas3 libcairo2 libdeflate0
324s   liberror-perl libfontconfig1 libfontenc1 libgfortran5 libgomp1
324s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
324s   liblapack3 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64
324s   libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal
324s   libpython3.11-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
324s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+
324s   ncbi-blast+-legacy ncbi-data python3-biopython python3-cairo python3-cgecore
324s   python3-cgelib python3-dateutil python3-freetype python3-git python3-gitdb
324s   python3-numpy python3-pandas python3-pandas-lib python3-pil
324s   python3-reportlab python3-rlpycairo python3-smmap python3-tabulate
324s   python3.11 python3.11-minimal resfinder resfinder-db resfinder-example
324s   sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
324s Suggested packages:
324s   fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre git-daemon-run
324s   | git-daemon-sysvinit git-doc git-email git-gui gitk gitweb git-cvs
324s   git-mediawiki git-svn liblcms2-utils python3-tk bwa clustalo clustalw
324s   dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons
324s   python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib
324s   python3-psycopg2 python3-scipy raxml samtools t-coffee wise python-git-doc
324s   gcc gfortran python3-dev python3-pytest python-pandas-doc
324s   python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools
324s   python-reportlab-doc rl-accel rl-renderpm python3.11-venv python3.11-doc
324s   binfmt-support sgml-base-doc debhelper
324s Recommended packages:
324s   python-biopython-doc python3-scipy python3-matplotlib python3-bottleneck
324s   python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib
324s   python3-lxml python3-tables python3-olefile
324s The following NEW packages will be installed:
324s   fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono
324s   fonts-urw-base35 git git-man kma libblas3 libcairo2 libdeflate0
324s   liberror-perl libfontconfig1 libfontenc1 libgfortran5 libgomp1
324s   libgraphite2-3 libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8
324s   liblapack3 liblcms2-2 liblerc4 libmbedcrypto7t64 libmbedtls14t64
324s   libmbedx509-1t64 libopenjp2-7 libpixman-1-0 libpython3.11-minimal
324s   libpython3.11-stdlib libraqm0 libsharpyuv0 libtiff6 libwebp7 libwebpdemux2
324s   libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 ncbi-blast+
324s   ncbi-blast+-legacy ncbi-data python3-biopython python3-cairo python3-cgecore
324s   python3-cgelib python3-dateutil python3-freetype python3-git python3-gitdb
324s   python3-numpy python3-pandas python3-pandas-lib python3-pil
324s   python3-reportlab python3-rlpycairo python3-smmap python3-tabulate
324s   python3.11 python3.11-minimal resfinder resfinder-db resfinder-example
324s   sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
324s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded.
324s 1 not fully installed or removed.
324s Need to get 79.1 MB of archives.
324s After this operation, 381 MB of additional disk space will be used.
324s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder-db all 0.0+git20220524.fa32d9a-1 [11.3 MB]
325s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
325s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
325s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
325s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
325s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
325s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
325s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
325s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
325s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
325s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
325s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
325s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
325s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
325s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
325s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
325s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
325s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
325s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
325s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
325s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
325s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
325s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
325s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
325s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
325s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
325s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
325s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
325s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
325s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB]
325s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
325s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
325s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB]
325s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB]
326s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
326s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
326s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
326s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
326s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
326s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
326s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
326s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB]
326s Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB]
326s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B]
326s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB]
326s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB]
326s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB]
326s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB]
326s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB]
326s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB]
326s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cgecore all 1.5.6+ds-1 [28.8 kB]
326s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tabulate all 0.8.10-1 [38.2 kB]
326s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
326s Get:54 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB]
326s Get:55 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB]
326s Get:56 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB]
326s Get:57 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB]
326s Get:58 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+-legacy all 2.12.0+ds-4build1 [4990 B]
326s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 kma arm64 1.4.14-2 [223 kB]
326s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 liberror-perl all 0.17029-2 [25.6 kB]
326s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 git-man all 1:2.43.0-1ubuntu1 [1100 kB]
326s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 git arm64 1:2.43.0-1ubuntu1 [3786 kB]
327s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-smmap all 6.0.0-1 [20.5 kB]
327s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-gitdb all 4.0.11-1 [46.2 kB]
327s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-git all 3.1.37-3 [138 kB]
327s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB]
327s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB]
327s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB]
327s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cgelib all 0.7.3-3 [48.2 kB]
327s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder all 4.4.2-1 [66.5 kB]
327s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 resfinder-example all 4.4.2-1 [572 kB]
328s Fetched 79.1 MB in 3s (25.6 MB/s)
328s Selecting previously unselected package resfinder-db.
328s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
328s Preparing to unpack .../00-resfinder-db_0.0+git20220524.fa32d9a-1_all.deb ...
328s Unpacking resfinder-db (0.0+git20220524.fa32d9a-1) ...
328s Selecting previously unselected package libpython3.11-minimal:arm64.
328s Preparing to unpack .../01-libpython3.11-minimal_3.11.8-1_arm64.deb ...
328s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ...
328s Selecting previously unselected package python3.11-minimal.
328s Preparing to unpack .../02-python3.11-minimal_3.11.8-1_arm64.deb ...
328s Unpacking python3.11-minimal (3.11.8-1) ...
328s Selecting previously unselected package libpython3.11-stdlib:arm64.
328s Preparing to unpack .../03-libpython3.11-stdlib_3.11.8-1_arm64.deb ...
328s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
328s Selecting previously unselected package python3.11.
328s Preparing to unpack .../04-python3.11_3.11.8-1_arm64.deb ...
328s Unpacking python3.11 (3.11.8-1) ...
328s Selecting previously unselected package libblas3:arm64.
328s Preparing to unpack .../05-libblas3_3.12.0-3_arm64.deb ...
328s Unpacking libblas3:arm64 (3.12.0-3) ...
328s Selecting previously unselected package libgfortran5:arm64.
328s Preparing to unpack .../06-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
328s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
328s Selecting previously unselected package liblapack3:arm64.
329s Preparing to unpack .../07-liblapack3_3.12.0-3_arm64.deb ...
329s Unpacking liblapack3:arm64 (3.12.0-3) ...
329s Selecting previously unselected package python3-numpy.
329s Preparing to unpack .../08-python3-numpy_1%3a1.24.2-2_arm64.deb ...
329s Unpacking python3-numpy (1:1.24.2-2) ...
329s Selecting previously unselected package libgomp1:arm64.
329s Preparing to unpack .../09-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
329s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
329s Selecting previously unselected package libimagequant0:arm64.
329s Preparing to unpack .../10-libimagequant0_2.18.0-1_arm64.deb ...
329s Unpacking libimagequant0:arm64 (2.18.0-1) ...
329s Selecting previously unselected package libjpeg-turbo8:arm64.
329s Preparing to unpack .../11-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
329s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
329s Selecting previously unselected package libjpeg8:arm64.
329s Preparing to unpack .../12-libjpeg8_8c-2ubuntu11_arm64.deb ...
329s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
329s Selecting previously unselected package liblcms2-2:arm64.
329s Preparing to unpack .../13-liblcms2-2_2.14-2_arm64.deb ...
329s Unpacking liblcms2-2:arm64 (2.14-2) ...
329s Selecting previously unselected package libopenjp2-7:arm64.
329s Preparing to unpack .../14-libopenjp2-7_2.5.0-2_arm64.deb ...
329s Unpacking libopenjp2-7:arm64 (2.5.0-2) ...
329s Selecting previously unselected package libgraphite2-3:arm64.
329s Preparing to unpack .../15-libgraphite2-3_1.3.14-2_arm64.deb ...
329s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
329s Selecting previously unselected package libharfbuzz0b:arm64.
329s Preparing to unpack .../16-libharfbuzz0b_8.3.0-2_arm64.deb ...
329s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
329s Selecting previously unselected package libraqm0:arm64.
329s Preparing to unpack .../17-libraqm0_0.10.1-1_arm64.deb ...
329s Unpacking libraqm0:arm64 (0.10.1-1) ...
329s Selecting previously unselected package libdeflate0:arm64.
329s Preparing to unpack .../18-libdeflate0_1.19-1_arm64.deb ...
329s Unpacking libdeflate0:arm64 (1.19-1) ...
329s Selecting previously unselected package libjbig0:arm64.
329s Preparing to unpack .../19-libjbig0_2.1-6.1ubuntu1_arm64.deb ...
329s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
329s Selecting previously unselected package liblerc4:arm64.
329s Preparing to unpack .../20-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ...
329s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
329s Selecting previously unselected package libsharpyuv0:arm64.
329s Preparing to unpack .../21-libsharpyuv0_1.3.2-0.4_arm64.deb ...
329s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
329s Selecting previously unselected package libwebp7:arm64.
329s Preparing to unpack .../22-libwebp7_1.3.2-0.4_arm64.deb ...
329s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
329s Selecting previously unselected package libtiff6:arm64.
329s Preparing to unpack .../23-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ...
329s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
329s Selecting previously unselected package libwebpdemux2:arm64.
329s Preparing to unpack .../24-libwebpdemux2_1.3.2-0.4_arm64.deb ...
329s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
329s Selecting previously unselected package libwebpmux3:arm64.
329s Preparing to unpack .../25-libwebpmux3_1.3.2-0.4_arm64.deb ...
329s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
329s Selecting previously unselected package python3-pil:arm64.
329s Preparing to unpack .../26-python3-pil_10.2.0-1_arm64.deb ...
329s Unpacking python3-pil:arm64 (10.2.0-1) ...
329s Selecting previously unselected package fonts-dejavu-mono.
329s Preparing to unpack .../27-fonts-dejavu-mono_2.37-8_all.deb ...
329s Unpacking fonts-dejavu-mono (2.37-8) ...
330s Selecting previously unselected package fonts-dejavu-core.
330s Preparing to unpack .../28-fonts-dejavu-core_2.37-8_all.deb ...
330s Unpacking fonts-dejavu-core (2.37-8) ...
330s Selecting previously unselected package libfontenc1:arm64.
330s Preparing to unpack .../29-libfontenc1_1%3a1.1.8-1_arm64.deb ...
330s Unpacking libfontenc1:arm64 (1:1.1.8-1) ...
330s Selecting previously unselected package x11-common.
330s Preparing to unpack .../30-x11-common_1%3a7.7+23ubuntu2_all.deb ...
330s Unpacking x11-common (1:7.7+23ubuntu2) ...
330s Selecting previously unselected package xfonts-encodings.
330s Preparing to unpack .../31-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
330s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
330s Selecting previously unselected package xfonts-utils.
330s Preparing to unpack .../32-xfonts-utils_1%3a7.7+6build2_arm64.deb ...
330s Unpacking xfonts-utils (1:7.7+6build2) ...
330s Selecting previously unselected package fonts-urw-base35.
330s Preparing to unpack .../33-fonts-urw-base35_20200910-8_all.deb ...
330s Unpacking fonts-urw-base35 (20200910-8) ...
330s Selecting previously unselected package fontconfig-config.
330s Preparing to unpack .../34-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
330s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
330s Selecting previously unselected package libfontconfig1:arm64.
330s Preparing to unpack .../35-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
330s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
330s Selecting previously unselected package libpixman-1-0:arm64.
330s Preparing to unpack .../36-libpixman-1-0_0.42.2-1_arm64.deb ...
330s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
330s Selecting previously unselected package libxcb-render0:arm64.
330s Preparing to unpack .../37-libxcb-render0_1.15-1_arm64.deb ...
330s Unpacking libxcb-render0:arm64 (1.15-1) ...
330s Selecting previously unselected package libxcb-shm0:arm64.
330s Preparing to unpack .../38-libxcb-shm0_1.15-1_arm64.deb ...
330s Unpacking libxcb-shm0:arm64 (1.15-1) ...
330s Selecting previously unselected package libxrender1:arm64.
330s Preparing to unpack .../39-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
330s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
330s Selecting previously unselected package libcairo2:arm64.
330s Preparing to unpack .../40-libcairo2_1.18.0-1_arm64.deb ...
330s Unpacking libcairo2:arm64 (1.18.0-1) ...
330s Selecting previously unselected package python3-cairo.
330s Preparing to unpack .../41-python3-cairo_1.25.1-2_arm64.deb ...
330s Unpacking python3-cairo (1.25.1-2) ...
330s Selecting previously unselected package python3-freetype.
330s Preparing to unpack .../42-python3-freetype_2.4.0-1_all.deb ...
330s Unpacking python3-freetype (2.4.0-1) ...
330s Selecting previously unselected package python3-rlpycairo.
330s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ...
330s Unpacking python3-rlpycairo (0.3.0-3) ...
330s Selecting previously unselected package fonts-dejavu-extra.
330s Preparing to unpack .../44-fonts-dejavu-extra_2.37-8_all.deb ...
330s Unpacking fonts-dejavu-extra (2.37-8) ...
331s Selecting previously unselected package python3-reportlab.
331s Preparing to unpack .../45-python3-reportlab_4.1.0-1_all.deb ...
331s Unpacking python3-reportlab (4.1.0-1) ...
331s Selecting previously unselected package sgml-base.
331s Preparing to unpack .../46-sgml-base_1.31_all.deb ...
331s Unpacking sgml-base (1.31) ...
331s Selecting previously unselected package xml-core.
331s Preparing to unpack .../47-xml-core_0.19_all.deb ...
331s Unpacking xml-core (0.19) ...
331s Selecting previously unselected package w3c-sgml-lib.
331s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ...
331s Unpacking w3c-sgml-lib (1.3-3) ...
331s Selecting previously unselected package python3-biopython.
331s Preparing to unpack .../49-python3-biopython_1.81+dfsg-3_arm64.deb ...
331s Unpacking python3-biopython (1.81+dfsg-3) ...
331s Selecting previously unselected package python3-cgecore.
331s Preparing to unpack .../50-python3-cgecore_1.5.6+ds-1_all.deb ...
331s Unpacking python3-cgecore (1.5.6+ds-1) ...
331s Selecting previously unselected package python3-tabulate.
331s Preparing to unpack .../51-python3-tabulate_0.8.10-1_all.deb ...
331s Unpacking python3-tabulate (0.8.10-1) ...
331s Selecting previously unselected package ncbi-data.
331s Preparing to unpack .../52-ncbi-data_6.1.20170106+dfsg1-10_all.deb ...
331s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
331s Selecting previously unselected package libmbedcrypto7t64:arm64.
331s Preparing to unpack .../53-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ...
331s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ...
331s Selecting previously unselected package libmbedx509-1t64:arm64.
331s Preparing to unpack .../54-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ...
331s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ...
331s Selecting previously unselected package libmbedtls14t64:arm64.
331s Preparing to unpack .../55-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ...
331s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
331s Selecting previously unselected package ncbi-blast+.
331s Preparing to unpack .../56-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ...
331s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ...
332s Selecting previously unselected package ncbi-blast+-legacy.
332s Preparing to unpack .../57-ncbi-blast+-legacy_2.12.0+ds-4build1_all.deb ...
332s Unpacking ncbi-blast+-legacy (2.12.0+ds-4build1) ...
332s Selecting previously unselected package kma.
332s Preparing to unpack .../58-kma_1.4.14-2_arm64.deb ...
332s Unpacking kma (1.4.14-2) ...
332s Selecting previously unselected package liberror-perl.
332s Preparing to unpack .../59-liberror-perl_0.17029-2_all.deb ...
332s Unpacking liberror-perl (0.17029-2) ...
332s Selecting previously unselected package git-man.
332s Preparing to unpack .../60-git-man_1%3a2.43.0-1ubuntu1_all.deb ...
332s Unpacking git-man (1:2.43.0-1ubuntu1) ...
332s Selecting previously unselected package git.
332s Preparing to unpack .../61-git_1%3a2.43.0-1ubuntu1_arm64.deb ...
332s Unpacking git (1:2.43.0-1ubuntu1) ...
332s Selecting previously unselected package python3-smmap.
332s Preparing to unpack .../62-python3-smmap_6.0.0-1_all.deb ...
332s Unpacking python3-smmap (6.0.0-1) ...
332s Selecting previously unselected package python3-gitdb.
332s Preparing to unpack .../63-python3-gitdb_4.0.11-1_all.deb ...
332s Unpacking python3-gitdb (4.0.11-1) ...
332s Selecting previously unselected package python3-git.
332s Preparing to unpack .../64-python3-git_3.1.37-3_all.deb ...
332s Unpacking python3-git (3.1.37-3) ...
332s Selecting previously unselected package python3-dateutil.
332s Preparing to unpack .../65-python3-dateutil_2.8.2-3_all.deb ...
332s Unpacking python3-dateutil (2.8.2-3) ...
332s Selecting previously unselected package python3-pandas-lib:arm64.
332s Preparing to unpack .../66-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ...
332s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
332s Selecting previously unselected package python3-pandas.
332s Preparing to unpack .../67-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ...
332s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ...
332s Selecting previously unselected package python3-cgelib.
332s Preparing to unpack .../68-python3-cgelib_0.7.3-3_all.deb ...
332s Unpacking python3-cgelib (0.7.3-3) ...
332s Selecting previously unselected package resfinder.
332s Preparing to unpack .../69-resfinder_4.4.2-1_all.deb ...
332s Unpacking resfinder (4.4.2-1) ...
332s Selecting previously unselected package resfinder-example.
332s Preparing to unpack .../70-resfinder-example_4.4.2-1_all.deb ...
332s Unpacking resfinder-example (4.4.2-1) ...
333s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
333s Setting up liblcms2-2:arm64 (2.14-2) ...
333s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
333s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
333s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
333s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
333s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ...
333s Setting up resfinder-db (0.0+git20220524.fa32d9a-1) ...
333s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
333s Setting up libxcb-render0:arm64 (1.15-1) ...
333s Setting up x11-common (1:7.7+23ubuntu2) ...
333s Setting up libdeflate0:arm64 (1.19-1) ...
333s Setting up python3-tabulate (0.8.10-1) ...
333s Setting up libxcb-shm0:arm64 (1.15-1) ...
333s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
333s Setting up python3-freetype (2.4.0-1) ...
333s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
333s Setting up liberror-perl (0.17029-2) ...
333s Setting up libfontenc1:arm64 (1:1.1.8-1) ...
333s Setting up libblas3:arm64 (3.12.0-3) ...
333s 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
333s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
333s Setting up libimagequant0:arm64 (2.18.0-1) ...
333s Setting up fonts-dejavu-mono (2.37-8) ...
333s Setting up fonts-dejavu-core (2.37-8) ...
333s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
333s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
333s Setting up libwebp7:arm64 (1.3.2-0.4) ...
333s Setting up fonts-dejavu-extra (2.37-8) ...
333s Setting up kma (1.4.14-2) ...
333s Setting up libopenjp2-7:arm64 (2.5.0-2) ...
333s Setting up git-man (1:2.43.0-1ubuntu1) ...
333s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
333s Setting up python3-dateutil (2.8.2-3) ...
333s Setting up sgml-base (1.31) ...
333s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
333s Setting up resfinder-example (4.4.2-1) ...
333s Setting up libwebpmux3:arm64 (1.3.2-0.4) ...
333s Setting up python3-smmap (6.0.0-1) ...
334s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
334s Setting up python3.11-minimal (3.11.8-1) ...
334s Setting up liblapack3:arm64 (3.12.0-3) ...
334s 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
334s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ...
334s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
335s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ...
335s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
335s Setting up python3-gitdb (4.0.11-1) ...
335s Setting up xfonts-utils (1:7.7+6build2) ...
335s Setting up libraqm0:arm64 (0.10.1-1) ...
335s Setting up git (1:2.43.0-1ubuntu1) ...
335s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
335s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
335s Setting up xml-core (0.19) ...
335s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
335s Setting up python3.11 (3.11.8-1) ...
336s Setting up fonts-urw-base35 (20200910-8) ...
336s Setting up libcairo2:arm64 (1.18.0-1) ...
336s Setting up ncbi-blast+ (2.12.0+ds-4build1) ...
336s Setting up python3-pil:arm64 (10.2.0-1) ...
336s Setting up python3-git (3.1.37-3) ...
337s Setting up python3-numpy (1:1.24.2-2) ...
338s Setting up ncbi-blast+-legacy (2.12.0+ds-4build1) ...
338s Setting up python3-cairo (1.25.1-2) ...
338s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ...
338s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ...
346s Setting up python3-rlpycairo (0.3.0-3) ...
346s Setting up python3-reportlab (4.1.0-1) ...
347s Setting up python3-cgelib (0.7.3-3) ...
347s Processing triggers for libc-bin (2.39-0ubuntu2) ...
348s Processing triggers for systemd (255.2-3ubuntu2) ...
348s Processing triggers for man-db (2.12.0-3) ...
349s Processing triggers for sgml-base (1.31) ...
349s Setting up w3c-sgml-lib (1.3-3) ...
376s Setting up python3-biopython (1.81+dfsg-3) ...
377s Setting up python3-cgecore (1.5.6+ds-1) ...
377s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:242: SyntaxWarning: invalid escape sequence '\w'
377s   start = re.search("^-*(\w+)", align_query).start(1)
377s /usr/lib/python3/dist-packages/cgecore/cgefinder.py:243: SyntaxWarning: invalid escape sequence '\w'
377s   end = re.search("\w+(-*)$", align_query).start(1)
377s /usr/lib/python3/dist-packages/cgecore/utility.py:137: SyntaxWarning: invalid escape sequence '\{'
377s   """
377s /usr/lib/python3/dist-packages/cgecore/utility.py:491: SyntaxWarning: invalid escape sequence '\w'
377s   src = re.sub('[^\w/\-\.\*]', '', src)
377s /usr/lib/python3/dist-packages/cgecore/utility.py:492: SyntaxWarning: invalid escape sequence '\w'
377s   dst = re.sub('[^\w/\-\.\*]', '', dst)
377s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
377s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
377s /usr/lib/python3/dist-packages/cgecore/utility.py:493: SyntaxWarning: invalid escape sequence '\W'
377s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
377s /usr/lib/python3/dist-packages/cgecore/utility.py:520: SyntaxWarning: invalid escape sequence '\w'
377s   invalid_chars = re.findall('[^\w/\-\.\*]', os.path.basename(file_))
377s /usr/lib/python3/dist-packages/cgecore/utility.py:539: SyntaxWarning: invalid escape sequence '\w'
377s   src = re.sub('[^\w/\-\.\*]', '', src)
377s /usr/lib/python3/dist-packages/cgecore/utility.py:540: SyntaxWarning: invalid escape sequence '\w'
377s   dst = re.sub('[^\w/\-\.\*]', '', dst)
377s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
377s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
377s /usr/lib/python3/dist-packages/cgecore/utility.py:541: SyntaxWarning: invalid escape sequence '\W'
377s   if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
377s Setting up resfinder (4.4.2-1) ...
377s Setting up autopkgtest-satdep (0) ...
383s (Reading database ... 82424 files and directories currently installed.)
383s Removing autopkgtest-satdep (0) ...
385s autopkgtest [02:15:37]: test version-test: [-----------------------
386s PASS
387s autopkgtest [02:15:39]: test version-test: -----------------------]
387s version-test         PASS (superficial)
387s autopkgtest [02:15:39]: test version-test:  - - - - - - - - - - results - - - - - - - - - -
388s autopkgtest [02:15:40]: @@@@@@@@@@@@@@@@@@@@ summary
388s run-unit-test        PASS
388s version-test         PASS (superficial)
399s Creating nova instance adt-noble-arm64-resfinder-20240318-020912-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...
399s Creating nova instance adt-noble-arm64-resfinder-20240318-020912-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...