0s autopkgtest [17:04:26]: starting date and time: 2024-06-28 17:04:26+0000
  0s autopkgtest [17:04:26]: git checkout: 85adf9a1 setup-testbed: prevent /tmp from getting a tmpfs mount
  0s autopkgtest [17:04:26]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8qfn54hm/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest --apt-upgrade python-cogent --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-7.secgroup --name adt-oracular-amd64-python-cogent-20240628-170426-juju-7f2275-prod-proposed-migration-environment-3-36b8932b-66de-4ce2-99d3-dc37e7683df4 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.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/
 78s autopkgtest [17:05:44]: testbed dpkg architecture: amd64
 78s autopkgtest [17:05:44]: testbed apt version: 2.9.5
 78s autopkgtest [17:05:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 81s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB]
 81s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [49.0 kB]
 81s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [369 kB]
 81s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B]
 81s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7052 B]
 81s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [102 kB]
 81s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [83.4 kB]
 81s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [28.0 kB]
 81s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B]
 81s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [407 kB]
 81s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [230 kB]
 81s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7968 B]
 81s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B]
 81s Fetched 1406 kB in 0s (5483 kB/s)
 81s Reading package lists...
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 86s Calculating upgrade...
 86s The following packages will be upgraded:
 86s   base-files motd-news-config
 86s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 86s Need to get 80.7 kB of archives.
 86s After this operation, 3072 B of additional disk space will be used.
 86s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 motd-news-config all 13.3ubuntu2 [5416 B]
 86s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.3ubuntu2 [75.3 kB]
 87s Fetched 80.7 kB in 0s (3985 kB/s)
 87s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 74417 files and directories currently installed.)
 87s Preparing to unpack .../motd-news-config_13.3ubuntu2_all.deb ...
 87s Unpacking motd-news-config (13.3ubuntu2) over (13.1ubuntu1) ...
 87s Preparing to unpack .../base-files_13.3ubuntu2_amd64.deb ...
 87s Unpacking base-files (13.3ubuntu2) over (13.1ubuntu1) ...
 87s Setting up base-files (13.3ubuntu2) ...
 87s Updating /etc/profile to current default.
 88s motd-news.service is a disabled or a static unit not running, not starting it.
 88s Setting up motd-news-config (13.3ubuntu2) ...
 88s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu7) ...
 88s update-initramfs: deferring update (trigger activated)
 88s Processing triggers for install-info (7.1-3build2) ...
 88s Processing triggers for man-db (2.12.1-2) ...
 88s Processing triggers for initramfs-tools (0.142ubuntu28) ...
 88s update-initramfs: Generating /boot/initrd.img-6.8.0-31-generic
 88s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
 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.
 99s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease
 99s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease
 99s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease
 99s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease
100s Reading package lists...
101s Reading package lists...
101s Building dependency tree...
101s Reading state information...
101s Calculating upgrade...
101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
101s Reading package lists...
102s Building dependency tree...
102s Reading state information...
102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
102s autopkgtest [17:06:08]: rebooting testbed after setup commands that affected boot
106s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
119s autopkgtest [17:06:25]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024
122s autopkgtest [17:06:28]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cogent
124s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-cogent 2024.5.7a1+dfsg-1 (dsc) [3004 B]
124s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-cogent 2024.5.7a1+dfsg-1 (tar) [14.8 MB]
124s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-cogent 2024.5.7a1+dfsg-1 (diff) [12.0 kB]
124s gpgv: Signature made Thu Jun 27 01:04:00 2024 UTC
124s gpgv:                using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1
124s gpgv:                issuer "eamanu@debian.org"
124s gpgv: Can't check signature: No public key
124s dpkg-source: warning: cannot verify inline signature for ./python-cogent_2024.5.7a1+dfsg-1.dsc: no acceptable signature found
125s autopkgtest [17:06:31]: testing package python-cogent version 2024.5.7a1+dfsg-1
128s autopkgtest [17:06:34]: build not needed
143s autopkgtest [17:06:49]: test run-unit-test: preparing testbed
143s Reading package lists...
144s Building dependency tree...
144s Reading state information...
144s Starting pkgProblemResolver with broken count: 0
144s Starting 2 pkgProblemResolver with broken count: 0
144s Done
145s The following additional packages will be installed:
145s   blt fonts-lyx libblas3 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
145s   libhwloc15 libimagequant0 libjs-jquery libjs-jquery-ui libjs-requirejs
145s   libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2
145s   libllvm14t64 libopenjp2-7 libpfm4 libqhull-r8.0 libraqm0 libtbb12
145s   libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libtk8.6 libwebpdemux2 libwebpmux3
145s   libxft2 libxrender1 libxslt1.1 libxss1 llvm-14 llvm-14-linker-tools
145s   llvm-14-runtime python-cogent-doc python-matplotlib-data python3-appdirs
145s   python3-brotli python3-cogent3 python3-contourpy python3-cycler
145s   python3-dateutil python3-decorator python3-fastjsonschema python3-fonttools
145s   python3-fs python3-importlib-metadata python3-iniconfig python3-jupyter-core
145s   python3-kiwisolver python3-llvmlite python3-lxml python3-lz4
145s   python3-matplotlib python3-mpmath python3-nbformat python3-numba
145s   python3-numpy python3-packaging python3-pandas python3-pandas-lib
145s   python3-pbr python3-pil python3-pil.imagetk python3-platformdirs
145s   python3-plotly python3-pluggy python3-pytest python3-scipy python3-scitrack
145s   python3-stevedore python3-sympy python3-tenacity python3-tinydb python3-tk
145s   python3-tqdm python3-traitlets python3-ufolib2 python3-unicodedata2
145s   python3-zipp tk8.6-blt2.5 unicode-data x11-common
145s Suggested packages:
145s   blt-demo libhwloc-contrib-plugins libjs-jquery-ui-docs liblcms2-utils tcl8.6
145s   tk8.6 llvm-14-doc python-cycler-doc python-fastjsonschema-doc python3-pip
145s   llvmlite-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft
145s   ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
145s   python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip
145s   python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc
145s   python3-gmpy2 nvidia-cuda-toolkit gcc gfortran python-numpy-doc python3-dev
145s   python-pandas-doc python3-statsmodels python-pil-doc python3-ipykernel
145s   python-scipy-doc texlive-fonts-extra python-sympy-doc python-tenacity-doc
145s   tix python3-tk-dbg
145s Recommended packages:
145s   libhwloc-plugins javascript-common llvm-14-dev dialign ncbi-blast+-legacy
145s   python3-bs4 python3-cssselect python3-html5lib numba-doc python3-pip
145s   python3-bottleneck python3-numexpr python3-odf python3-openpyxl
145s   python3-tables python3-olefile g++ | c++-compiler isympy-common
145s The following NEW packages will be installed:
145s   autopkgtest-satdep blt fonts-lyx libblas3 libgfortran5 libgomp1
145s   libgraphite2-3 libharfbuzz0b libhwloc15 libimagequant0 libjs-jquery
145s   libjs-jquery-ui libjs-requirejs libjs-sphinxdoc libjs-underscore liblapack3
145s   liblbfgsb0 liblcms2-2 libllvm14t64 libopenjp2-7 libpfm4 libqhull-r8.0
145s   libraqm0 libtbb12 libtbbbind-2-5 libtbbmalloc2 libtcl8.6 libtk8.6
145s   libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 llvm-14
145s   llvm-14-linker-tools llvm-14-runtime python-cogent-doc
145s   python-matplotlib-data python3-appdirs python3-brotli python3-cogent3
145s   python3-contourpy python3-cycler python3-dateutil python3-decorator
145s   python3-fastjsonschema python3-fonttools python3-fs
145s   python3-importlib-metadata python3-iniconfig python3-jupyter-core
145s   python3-kiwisolver python3-llvmlite python3-lxml python3-lz4
145s   python3-matplotlib python3-mpmath python3-nbformat python3-numba
145s   python3-numpy python3-packaging python3-pandas python3-pandas-lib
145s   python3-pbr python3-pil python3-pil.imagetk python3-platformdirs
145s   python3-plotly python3-pluggy python3-pytest python3-scipy python3-scitrack
145s   python3-stevedore python3-sympy python3-tenacity python3-tinydb python3-tk
145s   python3-tqdm python3-traitlets python3-ufolib2 python3-unicodedata2
145s   python3-zipp tk8.6-blt2.5 unicode-data x11-common
145s 0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
145s Need to get 128 MB/128 MB of archives.
145s After this operation, 548 MB of additional disk space will be used.
145s Get:1 /tmp/autopkgtest.jXlpON/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B]
145s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB]
145s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
145s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
145s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
145s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
145s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB]
145s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB]
145s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B]
145s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.0-1 [171 kB]
145s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB]
145s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB]
145s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB]
145s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
145s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB]
145s Get:16 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhwloc15 amd64 2.10.0-1build1 [172 kB]
145s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB]
145s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
145s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
145s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
145s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-sphinxdoc all 7.2.6-8 [150 kB]
145s Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB]
145s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
145s Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB]
145s Get:25 http://ftpmaster.internal/ubuntu oracular/universe amd64 libllvm14t64 amd64 1:14.0.6-20 [24.0 MB]
145s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB]
145s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB]
145s Get:28 http://ftpmaster.internal/ubuntu oracular/universe amd64 libtbbmalloc2 amd64 2021.11.0-2ubuntu2 [60.5 kB]
145s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libtbbbind-2-5 amd64 2021.11.0-2ubuntu2 [16.4 kB]
145s Get:30 http://ftpmaster.internal/ubuntu oracular/universe amd64 libtbb12 amd64 2021.11.0-2ubuntu2 [106 kB]
145s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB]
145s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB]
145s Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB]
145s Get:34 http://ftpmaster.internal/ubuntu oracular/universe amd64 llvm-14-runtime amd64 1:14.0.6-20 [481 kB]
145s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 llvm-14-linker-tools amd64 1:14.0.6-20 [1342 kB]
145s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpfm4 amd64 4.13.0+git32-g0d4ed0e-1 [414 kB]
145s Get:37 http://ftpmaster.internal/ubuntu oracular/universe amd64 llvm-14 amd64 1:14.0.6-20 [12.7 MB]
146s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-requirejs all 2.3.6+ds+~2.1.37-1 [201 kB]
146s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-cogent-doc all 2024.5.7a1+dfsg-1 [17.3 MB]
146s Get:40 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB]
146s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB]
146s Get:42 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB]
146s Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB]
146s Get:44 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB]
146s Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.3.0-2 [457 kB]
146s Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB]
146s Get:47 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.3.0-2 [9224 B]
146s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB]
146s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB]
146s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B]
146s Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
146s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.12.0-2 [16.5 MB]
146s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB]
146s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB]
146s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB]
146s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB]
146s Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB]
146s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB]
146s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB]
146s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB]
147s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB]
147s Get:62 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB]
147s Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB]
147s Get:64 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB]
147s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-llvmlite amd64 0.42.0-1build2 [166 kB]
147s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-numba amd64 0.59.1+dfsg-1 [1770 kB]
147s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB]
147s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB]
147s Get:69 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fastjsonschema all 2.19.1-1 [19.7 kB]
147s Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-platformdirs all 4.2.1-1 [16.3 kB]
147s Get:71 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB]
147s Get:72 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jupyter-core all 5.3.2-2 [25.5 kB]
147s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-nbformat all 5.9.1-1 [41.2 kB]
147s Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tenacity all 8.4.1-1 [16.8 kB]
147s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-plotly all 5.20.0+dfsg-1 [2766 kB]
147s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scitrack all 2021.5.3-3 [9424 B]
147s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tinydb all 3.15.2-4 [16.6 kB]
147s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-tqdm all 4.66.4-1 [91.3 kB]
147s Get:79 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-zipp all 3.19.2-2 [10.2 kB]
147s Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-importlib-metadata all 7.1.0-1 [19.2 kB]
147s Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pbr all 5.11.1-0ubuntu1 [66.5 kB]
147s Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-stevedore all 1:5.1.0-0ubuntu1 [21.0 kB]
147s Get:83 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cogent3 amd64 2024.5.7a1+dfsg-1 [2055 kB]
147s Get:84 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B]
147s Get:85 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB]
147s Get:86 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB]
147s Fetched 128 MB in 2s (55.2 MB/s)
148s Selecting previously unselected package libtcl8.6:amd64.
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148s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ...
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148s Selecting previously unselected package libxrender1:amd64.
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148s Selecting previously unselected package libxft2:amd64.
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148s Selecting previously unselected package x11-common.
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148s Selecting previously unselected package libxss1:amd64.
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148s Selecting previously unselected package libtk8.6:amd64.
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148s Selecting previously unselected package tk8.6-blt2.5.
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148s Selecting previously unselected package libblas3:amd64.
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148s Selecting previously unselected package liblapack3:amd64.
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149s Selecting previously unselected package libtbb12:amd64.
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149s Selecting previously unselected package libwebpdemux2:amd64.
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149s Selecting previously unselected package libwebpmux3:amd64.
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149s Selecting previously unselected package libxslt1.1:amd64.
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149s Selecting previously unselected package libpfm4:amd64.
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150s Selecting previously unselected package python3-brotli.
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150s Selecting previously unselected package libopenjp2-7:amd64.
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151s Selecting previously unselected package python3-lxml:amd64.
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152s Selecting previously unselected package python3-lz4.
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152s Selecting previously unselected package python3-kiwisolver.
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152s Selecting previously unselected package python3-pandas-lib:amd64.
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156s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
156s Setting up liblcms2-2:amd64 (2.14-2build1) ...
156s Setting up python3-iniconfig (1.1.1-2) ...
156s Setting up libtbbmalloc2:amd64 (2021.11.0-2ubuntu2) ...
156s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
156s Setting up python3-lz4 (4.0.2+dfsg-1build4) ...
156s Setting up python3-pbr (5.11.1-0ubuntu1) ...
156s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ...
156s Setting up fonts-lyx (2.4.0-1) ...
156s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ...
156s Setting up python3-tenacity (8.4.1-1) ...
156s Setting up python3-tqdm (4.66.4-1) ...
156s Setting up python3-tinydb (3.15.2-4) ...
157s Setting up x11-common (1:7.7+23ubuntu3) ...
157s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ...
157s Setting up python3-zipp (3.19.2-2) ...
157s Setting up libgomp1:amd64 (14.1.0-1ubuntu1) ...
157s Setting up libjs-requirejs (2.3.6+ds+~2.1.37-1) ...
157s Setting up python3-platformdirs (4.2.1-1) ...
157s Setting up unicode-data (15.1.0-1) ...
157s Setting up python3-decorator (5.1.1-5) ...
157s Setting up libblas3:amd64 (3.12.0-3build1) ...
157s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
157s Setting up python3-packaging (24.0-1) ...
157s Setting up libpfm4:amd64 (4.13.0+git32-g0d4ed0e-1) ...
157s Setting up python3-brotli (1.1.0-2build2) ...
158s Setting up python3-cycler (0.12.1-1) ...
158s Setting up libimagequant0:amd64 (2.18.0-1build1) ...
158s Setting up python3-kiwisolver (1.4.5-1) ...
158s Setting up libhwloc15:amd64 (2.10.0-1build1) ...
158s Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ...
158s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ...
158s Setting up libllvm14t64:amd64 (1:14.0.6-20) ...
158s Setting up python3-pluggy (1.5.0-1) ...
158s Setting up python3-fastjsonschema (2.19.1-1) ...
158s Setting up python3-traitlets (5.5.0-2) ...
158s Setting up python3-scitrack (2021.5.3-3) ...
158s Setting up libxslt1.1:amd64 (1.1.39-0exp1build1) ...
158s Setting up libopenjp2-7:amd64 (2.5.0-2build3) ...
158s Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ...
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165s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
165s Setting up libxft2:amd64 (2.3.6-1build1) ...
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184s update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode
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189s Setting up python3-cogent3 (2024.5.7a1+dfsg-1) ...
190s Setting up autopkgtest-satdep (0) ...
190s Processing triggers for libc-bin (2.39-0ubuntu9) ...
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190s Processing triggers for man-db (2.12.1-2) ...
195s (Reading database ... 99272 files and directories currently installed.)
195s Removing autopkgtest-satdep (0) ...
195s autopkgtest [17:07:41]: test run-unit-test: [-----------------------
215s ============================= test session starts ==============================
215s platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0
215s rootdir: /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests
215s collected 11030 items
215s 
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361s test_format/test_clustal.py ...                                          [ 90%]
361s test_format/test_fasta.py .                                              [ 90%]
361s test_maths/test_distance_transform.py .................................. [ 91%]
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464s test_util/test_io.py ...................................ssss.sss         [ 97%]
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470s test_util/test_union_dict.py ...........                                 [ 99%]
470s test_util/test_warning.py .........................                      [100%]
470s 
470s =============================== warnings summary ===============================
470s test_app/test_evo.py:876
470s   /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests/test_app/test_evo.py:876: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
470s     @pytest.mark.internet
470s 
470s test_tree_distance.py:111
470s   /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests/test_tree_distance.py:111: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
470s     @pytest.mark.slow
470s 
470s test_util/test_io.py:313
470s   /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests/test_util/test_io.py:313: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
470s     @pytest.mark.internet
470s 
470s test_util/test_io.py:351
470s   /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests/test_util/test_io.py:351: PytestUnknownMarkWarning: Unknown pytest.mark.internet - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
470s     @pytest.mark.internet
470s 
470s test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general
470s   /tmp/autopkgtest.jXlpON/autopkgtest_tmp/tests/test_evolve/test_ns_substitution_model.py:109: UserWarning:
470s   
470s   FORCED EXIT from optimiser after 25 evaluations
470s 
470s test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch
470s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning:
470s   
470s   Degrees of freedom <= 0 for slice
470s 
470s test_util/test_deserialise.py::test_convert_annotation_to_annotation_db
470s test_util/test_deserialise.py::test_deserialise_old_style_annotated
470s test_util/test_deserialise.py::test_deserialise_old_style_annotated
470s test_util/test_deserialise.py::test_deserialise_old_style_annotated
470s test_util/test_deserialise.py::test_deserialise_old_style_annotated
470s test_util/test_deserialise.py::test_deser_annotated_aln
470s   /usr/lib/python3/dist-packages/cogent3/util/warning.py:226: DeprecationWarning:
470s   
470s   class Map is discontinued and will be removed in version 2024.6
470s   reason='Replaced by IndelMap and FeatureMap'
470s 
470s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
470s = 11018 passed, 9 skipped, 2 xfailed, 1 xpassed, 12 warnings in 264.17s (0:04:24) =
472s autopkgtest [17:12:18]: test run-unit-test: -----------------------]
472s autopkgtest [17:12:18]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
472s run-unit-test        PASS
472s autopkgtest [17:12:18]: @@@@@@@@@@@@@@@@@@@@ summary
472s run-unit-test        PASS
497s nova [W] Skipping flock for amd64
497s Creating nova instance adt-oracular-amd64-python-cogent-20240628-170426-juju-7f2275-prod-proposed-migration-environment-3-36b8932b-66de-4ce2-99d3-dc37e7683df4 from image adt/ubuntu-oracular-amd64-server-20240628.img (UUID 9d02b460-22c0-49a4-a380-3bb68f865fe5)...