0s autopkgtest [02:06:45]: starting date: 2024-03-18
  0s autopkgtest [02:06:45]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt
  0s autopkgtest [02:06:45]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fpey_5n8/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 python-biotools --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-arm64-5.secgroup --name adt-noble-arm64-python-biotools-20240318-020645-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/
 73s autopkgtest [02:07:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 73s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 74s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 74s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB]
 74s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
 74s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB]
 76s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB]
 76s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 76s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
 76s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 76s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB]
 76s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 76s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB]
 76s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 78s Fetched 9189 kB in 3s (2636 kB/s)
 78s Reading package lists...
 81s Reading package lists...
 81s Building dependency tree...
 81s Reading state information...
 82s Calculating upgrade...
 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 82s Reading package lists...
 82s Building dependency tree...
 82s Reading state information...
 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 84s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 84s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 84s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 84s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 85s Reading package lists...
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 86s Calculating upgrade...
 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 86s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 88s autopkgtest [02:08:13]: testbed dpkg architecture: arm64
 89s autopkgtest [02:08:14]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
 89s autopkgtest [02:08:14]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biotools
 90s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-biotools 1.2.12-5 (dsc) [2077 B]
 90s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-biotools 1.2.12-5 (tar) [25.4 kB]
 90s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-biotools 1.2.12-5 (diff) [7412 B]
 90s gpgv: Signature made Fri Dec 13 11:54:57 2019 UTC
 90s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 90s gpgv:                issuer "tille@debian.org"
 90s gpgv: Can't check signature: No public key
 90s dpkg-source: warning: cannot verify inline signature for ./python-biotools_1.2.12-5.dsc: no acceptable signature found
 91s autopkgtest [02:08:16]: testing package python-biotools version 1.2.12-5
 91s autopkgtest [02:08:16]: build not needed
 91s autopkgtest [02:08:16]: test autodep8-python3: preparing testbed
 93s Reading package lists...
 93s Building dependency tree...
 93s Reading state information...
 94s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
 94s Starting 2 pkgProblemResolver with broken count: 0
 94s Done
 94s  Done
 94s Starting pkgProblemResolver with broken count: 0
 94s Starting 2 pkgProblemResolver with broken count: 0
 94s Done
 95s The following additional packages will be installed:
 95s   blt clustalw fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx
 95s   libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
 95s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
 95s   libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64
 95s   libmbedtls14t64 libmbedx509-1t64 libopenjp2-7 libpython3.11-minimal
 95s   libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6
 95s   libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1
 95s   libxss1 ncbi-blast+ ncbi-data python-matplotlib-data python3-all
 95s   python3-appdirs python3-biotools python3-brotli python3-contourpy
 95s   python3-cycler python3-dateutil python3-decorator python3-distutils
 95s   python3-fonttools python3-fs python3-kiwisolver python3-lib2to3 python3-lxml
 95s   python3-lz4 python3-matplotlib python3-mpmath python3-numpy
 95s   python3-packaging python3-pil python3-pil.imagetk python3-scipy
 95s   python3-sympy python3-tk python3-ufolib2 python3.11 python3.11-minimal
 95s   tk8.6-blt2.5 unicode-data x11-common
 95s Suggested packages:
 95s   blt-demo clustalx seaview libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6
 95s   python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
 95s   fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
 95s   python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip
 95s   python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc
 95s   python3-gmpy2 gcc gfortran python3-dev python3-pytest python-pil-doc
 95s   python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg
 95s   python3.11-venv python3.11-doc binfmt-support
 95s Recommended packages:
 95s   javascript-common python3-bs4 python3-cssselect python3-html5lib
 95s   python3-olefile g++ | c++-compiler isympy-common
 95s The following NEW packages will be installed:
 95s   blt clustalw fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx
 95s   libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3
 95s   libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery
 95s   libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libmbedcrypto7t64
 95s   libmbedtls14t64 libmbedx509-1t64 libopenjp2-7 libpython3.11-minimal
 95s   libpython3.11-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libtcl8.6 libtiff6
 95s   libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1
 95s   libxss1 ncbi-blast+ ncbi-data python-matplotlib-data python3-all
 95s   python3-appdirs python3-biotools python3-brotli python3-contourpy
 95s   python3-cycler python3-dateutil python3-decorator python3-distutils
 95s   python3-fonttools python3-fs python3-kiwisolver python3-lib2to3 python3-lxml
 95s   python3-lz4 python3-matplotlib python3-mpmath python3-numpy
 95s   python3-packaging python3-pil python3-pil.imagetk python3-scipy
 95s   python3-sympy python3-tk python3-ufolib2 python3.11 python3.11-minimal
 95s   tk8.6-blt2.5 unicode-data x11-common
 95s 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded.
 95s 1 not fully installed or removed.
 95s Need to get 84.5 MB of archives.
 95s After this operation, 389 MB of additional disk space will be used.
 95s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB]
 96s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB]
 96s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B]
 96s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
 96s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
 96s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
 96s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
 96s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB]
 96s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB]
 96s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB]
 96s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
 96s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB]
 96s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
 96s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
 96s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB]
 96s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB]
 96s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
 96s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
 96s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB]
 96s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
 96s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
 96s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
 96s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
 96s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
 96s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
 96s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB]
 96s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB]
 96s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB]
 96s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
 96s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
 96s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
 96s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
 96s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
 96s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
 96s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
 96s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
 96s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB]
 96s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B]
 96s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB]
 96s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B]
 96s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB]
 96s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB]
 96s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB]
 96s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB]
 96s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
 96s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
 96s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
 96s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB]
 97s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB]
 97s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B]
 97s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB]
 97s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
 97s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB]
 97s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB]
 97s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB]
 97s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB]
 97s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB]
 97s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB]
 97s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB]
 97s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.35-1 [161 kB]
 97s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB]
 97s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB]
 97s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB]
 97s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB]
 97s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-1build2 [65.4 kB]
 97s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB]
 97s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB]
 97s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB]
 97s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 clustalw arm64 2.1+lgpl-7 [240 kB]
 97s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB]
 98s Get:71 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB]
 98s Get:72 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB]
 98s Get:73 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB]
 98s Get:74 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB]
 98s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biotools all 1.2.12-5 [28.9 kB]
 99s Fetched 84.5 MB in 3s (32.0 MB/s)
 99s Selecting previously unselected package python3-lib2to3.
 99s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 74758 files and directories currently installed.)
 99s Preparing to unpack .../00-python3-lib2to3_3.11.5-1_all.deb ...
 99s Unpacking python3-lib2to3 (3.11.5-1) ...
 99s Selecting previously unselected package python3-distutils.
 99s Preparing to unpack .../01-python3-distutils_3.11.5-1_all.deb ...
 99s Unpacking python3-distutils (3.11.5-1) ...
 99s Selecting previously unselected package python3-all.
 99s Preparing to unpack .../02-python3-all_3.12.1-0ubuntu2_arm64.deb ...
 99s Unpacking python3-all (3.12.1-0ubuntu2) ...
 99s Selecting previously unselected package libjs-jquery.
 99s Preparing to unpack .../03-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
 99s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
 99s Selecting previously unselected package libjs-jquery-ui.
 99s Preparing to unpack .../04-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
 99s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
 99s Selecting previously unselected package fonts-dejavu-mono.
 99s Preparing to unpack .../05-fonts-dejavu-mono_2.37-8_all.deb ...
 99s Unpacking fonts-dejavu-mono (2.37-8) ...
 99s Selecting previously unselected package fonts-dejavu-core.
 99s Preparing to unpack .../06-fonts-dejavu-core_2.37-8_all.deb ...
 99s Unpacking fonts-dejavu-core (2.37-8) ...
 99s Selecting previously unselected package fonts-lyx.
 99s Preparing to unpack .../07-fonts-lyx_2.4.0~RC3-1_all.deb ...
 99s Unpacking fonts-lyx (2.4.0~RC3-1) ...
 99s Selecting previously unselected package python-matplotlib-data.
 99s Preparing to unpack .../08-python-matplotlib-data_3.6.3-1ubuntu3_all.deb ...
 99s Unpacking python-matplotlib-data (3.6.3-1ubuntu3) ...
 99s Selecting previously unselected package python3-dateutil.
 99s Preparing to unpack .../09-python3-dateutil_2.8.2-3_all.deb ...
 99s Unpacking python3-dateutil (2.8.2-3) ...
 99s Selecting previously unselected package libgomp1:arm64.
 99s Preparing to unpack .../10-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
 99s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
 99s Selecting previously unselected package libimagequant0:arm64.
 99s Preparing to unpack .../11-libimagequant0_2.18.0-1_arm64.deb ...
 99s Unpacking libimagequant0:arm64 (2.18.0-1) ...
 99s Selecting previously unselected package libjpeg-turbo8:arm64.
 99s Preparing to unpack .../12-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
 99s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
 99s Selecting previously unselected package libjpeg8:arm64.
 99s Preparing to unpack .../13-libjpeg8_8c-2ubuntu11_arm64.deb ...
 99s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
 99s Selecting previously unselected package liblcms2-2:arm64.
 99s Preparing to unpack .../14-liblcms2-2_2.14-2_arm64.deb ...
 99s Unpacking liblcms2-2:arm64 (2.14-2) ...
 99s Selecting previously unselected package libopenjp2-7:arm64.
 99s Preparing to unpack .../15-libopenjp2-7_2.5.0-2_arm64.deb ...
 99s Unpacking libopenjp2-7:arm64 (2.5.0-2) ...
 99s Selecting previously unselected package libgraphite2-3:arm64.
 99s Preparing to unpack .../16-libgraphite2-3_1.3.14-2_arm64.deb ...
 99s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
 99s Selecting previously unselected package libharfbuzz0b:arm64.
 99s Preparing to unpack .../17-libharfbuzz0b_8.3.0-2_arm64.deb ...
 99s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
 99s Selecting previously unselected package libraqm0:arm64.
 99s Preparing to unpack .../18-libraqm0_0.10.1-1_arm64.deb ...
 99s Unpacking libraqm0:arm64 (0.10.1-1) ...
100s Selecting previously unselected package libdeflate0:arm64.
100s Preparing to unpack .../19-libdeflate0_1.19-1_arm64.deb ...
100s Unpacking libdeflate0:arm64 (1.19-1) ...
100s Selecting previously unselected package libjbig0:arm64.
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100s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ...
100s Selecting previously unselected package liblerc4:arm64.
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100s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
100s Selecting previously unselected package libsharpyuv0:arm64.
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100s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ...
100s Selecting previously unselected package libwebp7:arm64.
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100s Unpacking libwebp7:arm64 (1.3.2-0.4) ...
100s Selecting previously unselected package libtiff6:arm64.
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100s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
100s Selecting previously unselected package libwebpdemux2:arm64.
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100s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ...
100s Selecting previously unselected package libwebpmux3:arm64.
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100s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ...
100s Selecting previously unselected package python3-pil:arm64.
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100s Unpacking python3-pil:arm64 (10.2.0-1) ...
100s Selecting previously unselected package libtcl8.6:arm64.
100s Preparing to unpack .../28-libtcl8.6_8.6.13+dfsg-2_arm64.deb ...
100s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ...
100s Selecting previously unselected package fontconfig-config.
100s Preparing to unpack .../29-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
100s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
100s Selecting previously unselected package libfontconfig1:arm64.
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100s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
100s Selecting previously unselected package libxrender1:arm64.
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100s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
100s Selecting previously unselected package libxft2:arm64.
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100s Selecting previously unselected package x11-common.
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100s Selecting previously unselected package libxss1:arm64.
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100s Selecting previously unselected package libtk8.6:arm64.
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100s Unpacking libtk8.6:arm64 (8.6.13-2) ...
100s Selecting previously unselected package tk8.6-blt2.5.
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100s Selecting previously unselected package blt.
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100s Selecting previously unselected package python3-tk:arm64.
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100s Selecting previously unselected package python3-pil.imagetk:arm64.
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100s Selecting previously unselected package libpython3.11-minimal:arm64.
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100s Selecting previously unselected package python3.11-minimal.
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100s Unpacking python3.11-minimal (3.11.8-1) ...
100s Selecting previously unselected package libpython3.11-stdlib:arm64.
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100s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ...
101s Selecting previously unselected package python3.11.
101s Preparing to unpack .../43-python3.11_3.11.8-1_arm64.deb ...
101s Unpacking python3.11 (3.11.8-1) ...
101s Selecting previously unselected package libblas3:arm64.
101s Preparing to unpack .../44-libblas3_3.12.0-3_arm64.deb ...
101s Unpacking libblas3:arm64 (3.12.0-3) ...
101s Selecting previously unselected package libgfortran5:arm64.
101s Preparing to unpack .../45-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
101s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
101s Selecting previously unselected package liblapack3:arm64.
101s Preparing to unpack .../46-liblapack3_3.12.0-3_arm64.deb ...
101s Unpacking liblapack3:arm64 (3.12.0-3) ...
101s Selecting previously unselected package python3-numpy.
101s Preparing to unpack .../47-python3-numpy_1%3a1.24.2-2_arm64.deb ...
101s Unpacking python3-numpy (1:1.24.2-2) ...
101s Selecting previously unselected package python3-contourpy.
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101s Unpacking python3-contourpy (1.0.7-1build2) ...
101s Selecting previously unselected package python3-cycler.
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101s Unpacking python3-cycler (0.11.0-2) ...
101s Selecting previously unselected package python3-brotli.
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101s Unpacking python3-brotli (1.1.0-2) ...
101s Selecting previously unselected package python3-decorator.
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101s Unpacking python3-decorator (5.1.1-5) ...
101s Selecting previously unselected package liblbfgsb0:arm64.
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101s Selecting previously unselected package python3-scipy.
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101s Unpacking python3-scipy (1.11.4-6) ...
102s Selecting previously unselected package python3-ufolib2.
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102s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ...
102s Selecting previously unselected package python3-mpmath.
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102s Unpacking python3-sympy (1.12-7) ...
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102s Unpacking python3-appdirs (1.4.4-4) ...
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103s Selecting previously unselected package libxslt1.1:arm64.
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103s Selecting previously unselected package python3-lxml:arm64.
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103s Unpacking unicode-data (15.1.0-1) ...
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103s Unpacking python3-fonttools (4.46.0-1) ...
103s Selecting previously unselected package python3-kiwisolver.
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103s Unpacking python3-kiwisolver (1.4.4-1build2) ...
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103s Selecting previously unselected package python3-matplotlib.
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103s Selecting previously unselected package clustalw.
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103s Unpacking clustalw (2.1+lgpl-7) ...
103s Selecting previously unselected package ncbi-data.
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103s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ...
104s Selecting previously unselected package libmbedcrypto7t64:arm64.
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104s Selecting previously unselected package libmbedx509-1t64:arm64.
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104s Selecting previously unselected package libmbedtls14t64:arm64.
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104s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
104s Selecting previously unselected package ncbi-blast+.
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104s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ...
104s Selecting previously unselected package python3-biotools.
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104s Unpacking python3-biotools (1.2.12-5) ...
104s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
104s Setting up liblcms2-2:arm64 (2.14-2) ...
104s Setting up ncbi-data (6.1.20170106+dfsg1-10) ...
104s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
104s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ...
104s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ...
104s Setting up libxrender1:arm64 (1:0.9.10-1.1) ...
104s Setting up python3-lz4 (4.0.2+dfsg-1build2) ...
104s Setting up fonts-lyx (2.4.0~RC3-1) ...
104s Setting up x11-common (1:7.7+23ubuntu2) ...
105s Setting up libdeflate0:arm64 (1.19-1) ...
105s Setting up libqhull-r8.0:arm64 (2020.2-6) ...
105s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
105s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ...
105s Setting up unicode-data (15.1.0-1) ...
105s Setting up python3-decorator (5.1.1-5) ...
105s Setting up libblas3:arm64 (3.12.0-3) ...
105s 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
105s Setting up python3-packaging (23.2-1) ...
105s Setting up python3-brotli (1.1.0-2) ...
105s Setting up python3-cycler (0.11.0-2) ...
105s Setting up libimagequant0:arm64 (2.18.0-1) ...
105s Setting up fonts-dejavu-mono (2.37-8) ...
105s Setting up python3-kiwisolver (1.4.4-1build2) ...
105s Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ...
105s Setting up fonts-dejavu-core (2.37-8) ...
105s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
105s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
105s Setting up libwebp7:arm64 (1.3.2-0.4) ...
105s Setting up libxslt1.1:arm64 (1.1.35-1) ...
105s Setting up clustalw (2.1+lgpl-7) ...
105s Setting up libopenjp2-7:arm64 (2.5.0-2) ...
105s Setting up libharfbuzz0b:arm64 (8.3.0-2) ...
105s Setting up python3-dateutil (2.8.2-3) ...
105s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ...
105s Setting up libxss1:arm64 (1:1.2.3-1build2) ...
105s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
105s Setting up python3-mpmath (1.2.1-3) ...
106s Setting up python-matplotlib-data (3.6.3-1ubuntu3) ...
106s Setting up libwebpmux3:arm64 (1.3.2-0.4) ...
106s Setting up python3-lib2to3 (3.11.5-1) ...
106s Setting up python3-appdirs (1.4.4-4) ...
106s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
106s Setting up python3-distutils (3.11.5-1) ...
106s python3.12: can't get files for byte-compilation
106s Setting up python3.11-minimal (3.11.8-1) ...
107s Setting up python3-sympy (1.12-7) ...
112s Setting up liblapack3:arm64 (3.12.0-3) ...
112s 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
112s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ...
112s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
112s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ...
112s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ...
112s Setting up python3-all (3.12.1-0ubuntu2) ...
112s Setting up python3-fs (2.4.16-3) ...
113s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
113s Setting up libraqm0:arm64 (0.10.1-1) ...
113s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ...
113s Setting up python3-lxml:arm64 (5.1.0-1) ...
113s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ...
113s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
113s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ...
113s Setting up python3.11 (3.11.8-1) ...
113s Setting up libxft2:arm64 (2.3.6-1) ...
113s Setting up libtk8.6:arm64 (8.6.13-2) ...
113s Setting up ncbi-blast+ (2.12.0+ds-4build1) ...
113s Setting up python3-pil:arm64 (10.2.0-1) ...
114s Setting up python3-numpy (1:1.24.2-2) ...
115s Setting up python3-contourpy (1.0.7-1build2) ...
115s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
115s Setting up python3-scipy (1.11.4-6) ...
118s Setting up blt (2.5.3+dfsg-7) ...
118s Setting up python3-tk:arm64 (3.11.5-1) ...
118s Setting up python3-pil.imagetk:arm64 (10.2.0-1) ...
118s Setting up python3-fonttools (4.46.0-1) ...
119s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
119s Setting up python3-matplotlib (3.6.3-1ubuntu3) ...
120s Setting up python3-biotools (1.2.12-5) ...
120s Setting up autopkgtest-satdep (0) ...
120s Processing triggers for libc-bin (2.39-0ubuntu2) ...
120s Processing triggers for systemd (255.2-3ubuntu2) ...
121s Processing triggers for man-db (2.12.0-3) ...
126s (Reading database ... 82941 files and directories currently installed.)
126s Removing autopkgtest-satdep (0) ...
127s autopkgtest [02:08:52]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import biotools; print(biotools)" ; done
127s autopkgtest [02:08:52]: test autodep8-python3: [-----------------------
127s Testing with python3.12:
127s <module 'biotools' from '/usr/lib/python3/dist-packages/biotools/__init__.py'>
128s autopkgtest [02:08:53]: test autodep8-python3: -----------------------]
128s autopkgtest [02:08:53]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
128s autodep8-python3     PASS (superficial)
129s autopkgtest [02:08:54]: @@@@@@@@@@@@@@@@@@@@ summary
129s autodep8-python3     PASS (superficial)
132s Creating nova instance adt-noble-arm64-python-biotools-20240318-020645-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...