0s autopkgtest [09:48:16]: starting date and time: 2024-11-13 09:48:16+0000 0s autopkgtest [09:48:16]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:48:16]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mphpnkre/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade pairtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-29.secgroup --name adt-plucky-arm64-pairtools-20241113-094816-juju-7f2275-prod-proposed-migration-environment-20-9aae8141-5784-4e74-8990-ae79ae497caa --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 76s autopkgtest [09:49:32]: testbed dpkg architecture: arm64 76s autopkgtest [09:49:32]: testbed apt version: 2.9.8 76s autopkgtest [09:49:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 78s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 78s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 78s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 78s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 78s Fetched 1794 kB in 1s (1908 kB/s) 78s Reading package lists... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 82s The following NEW packages will be installed: 82s python3.13-gdbm 82s The following packages will be upgraded: 82s libpython3-stdlib python3 python3-gdbm python3-minimal 83s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 101 kB of archives. 83s After this operation, 141 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 83s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 83s Fetched 101 kB in 0s (277 kB/s) 84s (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 ... 79924 files and directories currently installed.) 84s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 84s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Setting up python3-minimal (3.12.7-1) ... 84s (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 ... 79924 files and directories currently installed.) 84s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 84s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 84s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Selecting previously unselected package python3.13-gdbm. 84s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 84s Unpacking python3.13-gdbm (3.13.0-2) ... 84s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 84s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 84s Setting up python3.13-gdbm (3.13.0-2) ... 84s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 84s Setting up python3 (3.12.7-1) ... 85s Setting up python3-gdbm:arm64 (3.12.7-1) ... 85s Processing triggers for man-db (2.12.1-3) ... 85s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 87s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 88s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s autopkgtest [09:49:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 94s autopkgtest [09:49:50]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 96s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (dsc) [2381 B] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (tar) [1255 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (diff) [7144 B] 97s gpgv: Signature made Wed Apr 10 17:37:23 2024 UTC 97s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 97s gpgv: Can't check signature: No public key 97s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.0.3-1build1.dsc: no acceptable signature found 97s autopkgtest [09:49:53]: testing package pairtools version 1.0.3-1build1 97s autopkgtest [09:49:53]: build not needed 97s autopkgtest [09:49:53]: test upstream-tests: preparing testbed 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 100s The following additional packages will be installed: 100s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 100s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 100s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 100s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 100s liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 100s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 100s libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-appdirs 100s python3-bioframe python3-brotli python3-click python3-colorama 100s python3-contourpy python3-cycler python3-dateutil python3-decorator 100s python3-fonttools python3-fs python3-iniconfig python3-kiwisolver 100s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 100s python3-packaging python3-pairtools python3-pandas python3-pandas-lib 100s python3-pil python3-pil.imagetk python3-pluggy python3-pysam python3-pytest 100s python3-scipy python3-six python3-sympy python3-tk python3-tz 100s python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13-tk 100s tk8.6-blt2.5 unicode-data x11-common 100s Suggested packages: 100s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 100s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 100s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 100s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 100s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 100s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev 100s python3-pairtools-examples python-pandas-doc python3-statsmodels 100s python-pil-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix 100s python3-tk-dbg 100s Recommended packages: 100s javascript-common python3-bs4 python3-cssselect python3-html5lib 100s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 100s python3-tables python3-olefile g++ | c++-compiler isympy-common 100s The following NEW packages will be installed: 100s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 100s fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 100s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 100s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 100s liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 100s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 100s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 100s python3-appdirs python3-bioframe python3-brotli python3-click 100s python3-colorama python3-contourpy python3-cycler python3-dateutil 100s python3-decorator python3-fonttools python3-fs python3-iniconfig 100s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 100s python3-mpmath python3-numpy python3-packaging python3-pairtools 100s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 100s python3-pluggy python3-pysam python3-pytest python3-scipy python3-six 100s python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 100s python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data x11-common 100s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 67.6 MB/67.6 MB of archives. 100s After this operation, 317 MB of additional disk space will be used. 100s Get:1 /tmp/autopkgtest.VnsOzp/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 101s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 101s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 101s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 101s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 101s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 101s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 101s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 101s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 101s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 101s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 101s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 101s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 101s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 101s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 101s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 101s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 101s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 101s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 101s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 101s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 101s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 101s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 101s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 101s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 101s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 102s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 102s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 102s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 102s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 102s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 102s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 102s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 102s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 102s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 102s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 102s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 102s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 102s Get:41 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 102s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 102s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 102s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 102s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 102s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 102s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 102s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 102s Get:49 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 102s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 102s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 102s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 102s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 102s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 102s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 102s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 103s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 103s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 103s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 103s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 103s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 103s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 103s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 103s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 103s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 104s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 104s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 104s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 104s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 104s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 104s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 104s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-bioframe all 0.4.1-1 [76.1 kB] 104s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 104s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 104s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 104s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 104s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pairtools arm64 1.0.3-1build1 [193 kB] 104s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 104s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 105s Fetched 67.6 MB in 4s (17.8 MB/s) 105s Selecting previously unselected package libtcl8.6:arm64. 105s (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 ... 79931 files and directories currently installed.) 105s Preparing to unpack .../00-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 105s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 105s Selecting previously unselected package fonts-dejavu-mono. 105s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-mono (2.37-8) ... 105s Selecting previously unselected package fonts-dejavu-core. 105s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 105s Unpacking fonts-dejavu-core (2.37-8) ... 105s Selecting previously unselected package fontconfig-config. 105s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 105s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 105s Selecting previously unselected package libfontconfig1:arm64. 105s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 105s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 105s Selecting previously unselected package libxrender1:arm64. 105s Preparing to unpack .../05-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 105s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 105s Selecting previously unselected package libxft2:arm64. 105s Preparing to unpack .../06-libxft2_2.3.6-1build1_arm64.deb ... 105s Unpacking libxft2:arm64 (2.3.6-1build1) ... 105s Selecting previously unselected package x11-common. 105s Preparing to unpack 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package libblas3:arm64. 106s Preparing to unpack .../13-libblas3_3.12.0-3build2_arm64.deb ... 106s Unpacking libblas3:arm64 (3.12.0-3build2) ... 106s Selecting previously unselected package libdeflate0:arm64. 106s Preparing to unpack .../14-libdeflate0_1.22-1_arm64.deb ... 106s Unpacking libdeflate0:arm64 (1.22-1) ... 106s Selecting previously unselected package libgfortran5:arm64. 106s Preparing to unpack .../15-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 106s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 106s Selecting previously unselected package libgomp1:arm64. 106s Preparing to unpack .../16-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 106s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 106s Selecting previously unselected package libgraphite2-3:arm64. 106s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 106s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 106s Selecting previously unselected package libharfbuzz0b:arm64. 106s Preparing to unpack .../18-libharfbuzz0b_10.0.1-1_arm64.deb ... 106s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 106s Selecting previously unselected package libhtscodecs2:arm64. 106s Preparing to unpack .../19-libhtscodecs2_1.6.1-1_arm64.deb ... 106s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 106s Selecting previously unselected package libhts3t64:arm64. 106s Preparing to unpack .../20-libhts3t64_1.20+ds-1_arm64.deb ... 106s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 106s Selecting previously unselected package libimagequant0:arm64. 106s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_arm64.deb ... 106s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 106s Selecting previously unselected package libjpeg-turbo8:arm64. 106s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 106s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 106s Selecting previously unselected package libjpeg8:arm64. 106s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_arm64.deb ... 106s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 106s Selecting previously unselected package libjs-jquery. 106s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 106s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 106s Selecting previously unselected package libjs-jquery-ui. 106s Preparing to unpack .../25-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 106s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 107s Selecting previously unselected package liblapack3:arm64. 107s Preparing to unpack .../26-liblapack3_3.12.0-3build2_arm64.deb ... 107s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 107s Selecting previously unselected package liblbfgsb0:arm64. 107s Preparing to unpack .../27-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 107s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 107s Selecting previously unselected package liblcms2-2:arm64. 107s Preparing to unpack .../28-liblcms2-2_2.16-2_arm64.deb ... 107s Unpacking liblcms2-2:arm64 (2.16-2) ... 107s Selecting previously unselected package liblerc4:arm64. 107s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 107s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 107s Selecting previously unselected package libqhull-r8.0:arm64. 107s Preparing to unpack .../30-libqhull-r8.0_2020.2-6build1_arm64.deb ... 107s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 107s Selecting previously unselected package libraqm0:arm64. 107s Preparing to unpack .../31-libraqm0_0.10.1-1build1_arm64.deb ... 107s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 107s Selecting previously unselected package libsharpyuv0:arm64. 107s Preparing to unpack .../32-libsharpyuv0_1.4.0-0.1_arm64.deb ... 107s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 107s Selecting previously unselected package libjbig0:arm64. 107s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 107s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 107s Selecting previously unselected package libwebp7:arm64. 107s Preparing to unpack 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package python3.12-tk. 108s Preparing to unpack .../45-python3.12-tk_3.12.7-3_arm64.deb ... 108s Unpacking python3.12-tk (3.12.7-3) ... 108s Selecting previously unselected package python3.13-tk. 108s Preparing to unpack .../46-python3.13-tk_3.13.0-2_arm64.deb ... 108s Unpacking python3.13-tk (3.13.0-2) ... 108s Selecting previously unselected package python3-tk:arm64. 108s Preparing to unpack .../47-python3-tk_3.12.7-1_arm64.deb ... 108s Unpacking python3-tk:arm64 (3.12.7-1) ... 108s Selecting previously unselected package python3-pil.imagetk:arm64. 108s Preparing to unpack .../48-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 108s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 108s Selecting previously unselected package python3-numpy. 108s Preparing to unpack .../49-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 108s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 108s Selecting previously unselected package python3-contourpy. 108s Preparing to unpack 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previously unselected package python3-matplotlib. 110s Preparing to unpack .../67-python3-matplotlib_3.8.3-3_arm64.deb ... 110s Unpacking python3-matplotlib (3.8.3-3) ... 110s Selecting previously unselected package python3-pandas-lib:arm64. 110s Preparing to unpack .../68-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 110s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 110s Selecting previously unselected package python3-pandas. 110s Preparing to unpack .../69-python3-pandas_2.2.3+dfsg-5_all.deb ... 110s Unpacking python3-pandas (2.2.3+dfsg-5) ... 111s Selecting previously unselected package python3-bioframe. 111s Preparing to unpack .../70-python3-bioframe_0.4.1-1_all.deb ... 111s Unpacking python3-bioframe (0.4.1-1) ... 111s Selecting previously unselected package python3-colorama. 111s Preparing to unpack .../71-python3-colorama_0.4.6-4_all.deb ... 111s Unpacking python3-colorama (0.4.6-4) ... 111s Selecting previously unselected package python3-click. 111s Preparing to unpack .../72-python3-click_8.1.7-2_all.deb ... 111s Unpacking python3-click (8.1.7-2) ... 111s Selecting previously unselected package python3-iniconfig. 111s Preparing to unpack .../73-python3-iniconfig_1.1.1-2_all.deb ... 111s Unpacking python3-iniconfig (1.1.1-2) ... 111s Selecting previously unselected package python3-pysam. 111s Preparing to unpack .../74-python3-pysam_0.22.1+ds-2_arm64.deb ... 111s Unpacking python3-pysam (0.22.1+ds-2) ... 111s Selecting previously unselected package python3-pairtools. 111s Preparing to unpack .../75-python3-pairtools_1.0.3-1build1_arm64.deb ... 111s Unpacking python3-pairtools (1.0.3-1build1) ... 111s Selecting previously unselected package python3-pluggy. 111s Preparing to unpack .../76-python3-pluggy_1.5.0-1_all.deb ... 111s Unpacking python3-pluggy (1.5.0-1) ... 111s Selecting previously unselected package python3-pytest. 111s Preparing to unpack .../77-python3-pytest_8.3.3-1_all.deb ... 111s Unpacking python3-pytest (8.3.3-1) ... 111s Selecting previously unselected package autopkgtest-satdep. 111s Preparing to unpack .../78-1-autopkgtest-satdep.deb ... 111s Unpacking autopkgtest-satdep (0) ... 111s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 111s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 111s Setting up liblcms2-2:arm64 (2.16-2) ... 111s Setting up python3-iniconfig (1.1.1-2) ... 112s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 112s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 112s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 112s Setting up python3-colorama (0.4.6-4) ... 112s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 112s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 112s Setting up fonts-lyx (2.4.2.1-1) ... 112s Setting up x11-common (1:7.7+23ubuntu3) ... 112s Setting up libdeflate0:arm64 (1.22-1) ... 112s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 112s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 112s Setting up python3-click (8.1.7-2) ... 112s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 112s Setting up python3-tz (2024.1-2) ... 113s Setting up unicode-data (15.1.0-1) ... 113s Setting up python3-six (1.16.0-7) ... 113s Setting up python3-decorator (5.1.1-5) ... 113s Setting up libblas3:arm64 (3.12.0-3build2) ... 113s 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 113s Setting up python3-packaging (24.1-1) ... 113s Setting up python3-brotli (1.1.0-2build2) ... 113s Setting up python3-cycler (0.12.1-1) ... 113s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 113s Setting up fonts-dejavu-mono (2.37-8) ... 113s Setting up python3-kiwisolver (1.4.7-2) ... 113s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 113s Setting up fonts-dejavu-core (2.37-8) ... 114s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 114s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 114s Setting up python3-pluggy (1.5.0-1) ... 114s Setting up libwebp7:arm64 (1.4.0-0.1) ... 114s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 114s Setting up libhts3t64:arm64 (1.20+ds-1) ... 114s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 114s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 114s Setting up python3-dateutil (2.9.0-2) ... 114s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 114s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 114s Setting up python3-mpmath (1.3.0-1) ... 115s Setting up python-matplotlib-data (3.8.3-3) ... 115s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 115s Setting up python3-appdirs (1.4.4-4) ... 115s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 115s Setting up python3-sympy (1.13.3-1) ... 122s Setting up liblapack3:arm64 (3.12.0-3build2) ... 122s 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 122s Setting up python3-pysam (0.22.1+ds-2) ... 122s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 123s Setting up python3-pytest (8.3.3-1) ... 123s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 123s Setting up python3-fs (2.4.16-4) ... 123s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 123s Setting up libraqm0:arm64 (0.10.1-1build1) ... 123s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 126s Setting up python3-lxml:arm64 (5.3.0-1) ... 126s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 126s Setting up python3-contourpy (1.3.0-2) ... 126s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 126s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 126s Setting up libxft2:arm64 (2.3.6-1build1) ... 126s Setting up python3-scipy (1.13.1-5) ... 130s Setting up libtk8.6:arm64 (8.6.15-1) ... 130s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 130s Setting up python3.12-tk (3.12.7-3) ... 130s Setting up python3.13-tk (3.13.0-2) ... 130s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 130s Setting up python3-pandas (2.2.3+dfsg-5) ... 136s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 136s Setting up blt (2.5.3+dfsg-7build1) ... 136s Setting up python3-tk:arm64 (3.12.7-1) ... 136s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 136s Setting up python3-fonttools (4.46.0-1build2) ... 138s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 138s Setting up python3-matplotlib (3.8.3-3) ... 139s Setting up python3-bioframe (0.4.1-1) ... 140s Setting up python3-pairtools (1.0.3-1build1) ... 140s /usr/lib/python3/dist-packages/pairtools/cli/select.py:90: SyntaxWarning: invalid escape sequence '\d' 140s """Select pairs according to some condition. 140s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:928: SyntaxWarning: invalid escape sequence '\w' 140s """Extract the name of the tile for each read name in the series 140s Setting up autopkgtest-satdep (0) ... 140s Processing triggers for libc-bin (2.40-1ubuntu3) ... 140s Processing triggers for man-db (2.12.1-3) ... 146s (Reading database ... 89356 files and directories currently installed.) 146s Removing autopkgtest-satdep (0) ... 148s autopkgtest [09:50:44]: test upstream-tests: [----------------------- 148s 148s rm -rf pairtools 148s 148s pytest-3 --ignore=.pc 150s ============================= test session starts ============================== 150s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 150s rootdir: /tmp/autopkgtest.VnsOzp/build.vS2/src 150s configfile: pytest.ini 150s testpaths: tests 150s plugins: typeguard-4.4.1 150s collected 31 items 150s 154s tests/test_dedup.py . [ 3%] 159s tests/test_filterbycov.py . [ 6%] 160s tests/test_flip.py . [ 9%] 161s tests/test_header.py . [ 12%] 162s tests/test_headerops.py ....... [ 35%] 163s tests/test_markasdup.py . [ 38%] 169s tests/test_merge.py . [ 41%] 172s tests/test_parse.py ... [ 51%] 176s tests/test_parse2.py .. [ 58%] 177s tests/test_restrict.py . [ 61%] 180s tests/test_scaling.py . [ 64%] 189s tests/test_select.py ....... [ 87%] 190s tests/test_sort.py . [ 90%] 192s tests/test_split.py . [ 93%] 201s tests/test_stats.py .. [100%] 201s 201s =============================== warnings summary =============================== 201s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 201s /usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 201s import pipes 201s 201s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 201s ======================== 31 passed, 1 warning in 52.13s ======================== 201s 201s echo ALL PASS 201s ALL PASS 201s autopkgtest [09:51:37]: test upstream-tests: -----------------------] 202s autopkgtest [09:51:38]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 202s upstream-tests PASS 202s autopkgtest [09:51:38]: @@@@@@@@@@@@@@@@@@@@ summary 202s upstream-tests PASS 253s nova [W] Skipping flock in bos03-arm64 253s Creating nova instance adt-plucky-arm64-pairtools-20241113-094816-juju-7f2275-prod-proposed-migration-environment-20-9aae8141-5784-4e74-8990-ae79ae497caa from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...