0s autopkgtest [09:47:45]: starting date and time: 2024-11-13 09:47:45+0000 0s autopkgtest [09:47:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:47:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m5f3fo5s/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-13.secgroup --name adt-plucky-amd64-pairtools-20241113-091106-juju-7f2275-prod-proposed-migration-environment-20-4689d2f9-778b-4bd0-9428-61299f0c6c0c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 1474s autopkgtest [10:12:19]: testbed dpkg architecture: amd64 1475s autopkgtest [10:12:20]: testbed apt version: 2.9.8 1475s autopkgtest [10:12:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1476s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 1476s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 1476s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 1476s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 1476s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 1476s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 1476s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 1476s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 1476s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 1476s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB] 1476s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 1476s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 1476s Fetched 2175 kB in 1s (2492 kB/s) 1476s Reading package lists... 1479s Reading package lists... 1479s Building dependency tree... 1479s Reading state information... 1479s Calculating upgrade... 1479s The following NEW packages will be installed: 1479s python3.13-gdbm 1479s The following packages will be upgraded: 1479s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 1479s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1479s Need to get 253 kB of archives. 1479s After this operation, 147 kB of additional disk space will be used. 1479s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 1480s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 1480s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 1480s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 1480s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 1480s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 1480s Fetched 253 kB in 0s (507 kB/s) 1480s (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 ... 75541 files and directories currently installed.) 1480s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 1480s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 1480s Setting up python3-minimal (3.12.7-1) ... 1481s (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 ... 75541 files and directories currently installed.) 1481s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 1481s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1481s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 1481s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 1481s Selecting previously unselected package python3.13-gdbm. 1481s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 1481s Unpacking python3.13-gdbm (3.13.0-2) ... 1481s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 1481s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 1481s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 1481s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 1481s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 1481s Setting up python3.13-gdbm (3.13.0-2) ... 1481s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 1481s Setting up python3 (3.12.7-1) ... 1481s Setting up python3-gdbm:amd64 (3.12.7-1) ... 1481s Processing triggers for man-db (2.12.1-3) ... 1481s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1482s Reading package lists... 1482s Building dependency tree... 1482s Reading state information... 1482s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1482s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 1483s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 1483s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 1483s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 1483s Reading package lists... 1483s Reading package lists... 1484s Building dependency tree... 1484s Reading state information... 1484s Calculating upgrade... 1484s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1484s Reading package lists... 1484s Building dependency tree... 1484s Reading state information... 1484s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1487s autopkgtest [10:12:32]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 1487s autopkgtest [10:12:32]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 1490s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (dsc) [2381 B] 1490s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (tar) [1255 kB] 1490s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.0.3-1build1 (diff) [7144 B] 1490s gpgv: Signature made Wed Apr 10 17:37:23 2024 UTC 1490s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 1490s gpgv: Can't check signature: No public key 1490s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.0.3-1build1.dsc: no acceptable signature found 1490s autopkgtest [10:12:35]: testing package pairtools version 1.0.3-1build1 1490s autopkgtest [10:12:35]: build not needed 1491s autopkgtest [10:12:36]: test upstream-tests: preparing testbed 1494s Reading package lists... 1495s Building dependency tree... 1495s Reading state information... 1495s Starting pkgProblemResolver with broken count: 0 1495s Starting 2 pkgProblemResolver with broken count: 0 1495s Done 1495s The following additional packages will be installed: 1495s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 1495s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 1495s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 1495s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 1495s liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 1495s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 1495s libxrender1 libxslt1.1 libxss1 python-matplotlib-data python3-appdirs 1495s python3-bioframe python3-brotli python3-click python3-colorama 1495s python3-contourpy python3-cycler python3-dateutil python3-decorator 1495s python3-fonttools python3-fs python3-iniconfig python3-kiwisolver 1496s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-numpy 1496s python3-packaging python3-pairtools python3-pandas python3-pandas-lib 1496s python3-pil python3-pil.imagetk python3-pluggy python3-pysam python3-pytest 1496s python3-scipy python3-six python3-sympy python3-tk python3-tz 1496s python3-ufolib2 python3-unicodedata2 python3.12-tk python3.13-tk 1496s tk8.6-blt2.5 unicode-data x11-common 1496s Suggested packages: 1496s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 1496s python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript 1496s gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc 1496s python3-cairocffi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip 1496s python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc 1496s python3-gmpy2 gcc gfortran python-numpy-doc python3-dev 1496s python3-pairtools-examples python-pandas-doc python3-statsmodels 1496s python-pil-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix 1496s python3-tk-dbg 1496s Recommended packages: 1496s javascript-common python3-bs4 python3-cssselect python3-html5lib 1496s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 1496s python3-tables python3-numba python3-olefile g++ | c++-compiler 1496s isympy-common 1496s The following NEW packages will be installed: 1496s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 1496s fonts-lyx libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 1496s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 1496s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 1496s liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 1496s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 1496s libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 1496s python3-appdirs python3-bioframe python3-brotli python3-click 1496s python3-colorama python3-contourpy python3-cycler python3-dateutil 1496s python3-decorator python3-fonttools python3-fs python3-iniconfig 1496s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 1496s python3-mpmath python3-numpy python3-packaging python3-pairtools 1496s python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk 1496s python3-pluggy python3-pysam python3-pytest python3-scipy python3-six 1496s python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 1496s python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data x11-common 1496s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 1496s Need to get 72.6 MB/72.6 MB of archives. 1496s After this operation, 337 MB of additional disk space will be used. 1496s Get:1 /tmp/autopkgtest.qrAS67/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 1496s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 1496s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 1497s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 1497s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 1497s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 1497s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 1497s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 1497s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1497s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 1497s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 1497s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 1497s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 1497s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 1497s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 1497s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 1497s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 1498s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 1498s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 1498s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 1498s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 1498s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 1498s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 1498s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 1498s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 1498s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 1498s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 1498s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 1498s Get:29 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 1498s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 1498s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 1498s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 1498s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 1498s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 1498s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 1498s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 1498s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 1498s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 1498s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 1498s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 1498s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 1499s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 1499s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 1499s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 1499s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 1499s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 1499s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 1499s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 1499s Get:49 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 1499s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 1499s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 1499s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 1499s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 1499s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 1499s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 1499s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 1500s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 1500s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 1500s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 1500s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 1500s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 1500s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 1500s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 1500s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 1500s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 1500s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 1501s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 1501s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 1501s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 1501s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 1501s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 1501s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bioframe all 0.4.1-1 [76.1 kB] 1501s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 1501s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 1501s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 1501s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 1501s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pairtools amd64 1.0.3-1build1 [201 kB] 1501s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 1501s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 1501s Fetched 72.6 MB in 5s (13.5 MB/s) 1501s Selecting previously unselected package libtcl8.6:amd64. 1501s (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 ... 75548 files and directories currently installed.) 1501s Preparing to unpack .../00-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 1501s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 1501s Selecting previously unselected package fonts-dejavu-mono. 1501s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 1501s Unpacking fonts-dejavu-mono (2.37-8) ... 1501s Selecting previously unselected package fonts-dejavu-core. 1501s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 1501s Unpacking fonts-dejavu-core (2.37-8) ... 1501s Selecting previously unselected package fontconfig-config. 1501s Preparing to unpack .../03-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 1502s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 1502s Selecting previously unselected package libfontconfig1:amd64. 1502s Preparing to unpack .../04-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 1502s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1502s Selecting previously unselected package libxrender1:amd64. 1502s Preparing to unpack .../05-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 1502s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 1502s Selecting previously unselected package libxft2:amd64. 1502s Preparing to unpack .../06-libxft2_2.3.6-1build1_amd64.deb ... 1502s Unpacking libxft2:amd64 (2.3.6-1build1) ... 1502s Selecting previously unselected package x11-common. 1502s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1502s Unpacking x11-common (1:7.7+23ubuntu3) ... 1502s Selecting previously unselected package libxss1:amd64. 1502s Preparing to unpack .../08-libxss1_1%3a1.2.3-1build3_amd64.deb ... 1502s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 1502s Selecting previously unselected package libtk8.6:amd64. 1502s Preparing to unpack .../09-libtk8.6_8.6.15-1_amd64.deb ... 1502s Unpacking libtk8.6:amd64 (8.6.15-1) ... 1502s Selecting previously unselected package tk8.6-blt2.5. 1502s Preparing to unpack .../10-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 1502s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1502s Selecting previously unselected package blt. 1502s Preparing to unpack .../11-blt_2.5.3+dfsg-7build1_amd64.deb ... 1502s Unpacking blt (2.5.3+dfsg-7build1) ... 1502s Selecting previously unselected package fonts-lyx. 1502s Preparing to unpack .../12-fonts-lyx_2.4.2.1-1_all.deb ... 1502s Unpacking fonts-lyx (2.4.2.1-1) ... 1502s Selecting previously unselected package libblas3:amd64. 1502s Preparing to unpack .../13-libblas3_3.12.0-3build2_amd64.deb ... 1502s Unpacking libblas3:amd64 (3.12.0-3build2) ... 1502s Selecting previously unselected package libdeflate0:amd64. 1502s Preparing to unpack .../14-libdeflate0_1.22-1_amd64.deb ... 1502s Unpacking libdeflate0:amd64 (1.22-1) ... 1502s Selecting previously unselected package libgfortran5:amd64. 1502s Preparing to unpack .../15-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 1502s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1502s Selecting previously unselected package libgomp1:amd64. 1502s Preparing to unpack .../16-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 1502s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 1502s Selecting previously unselected package libgraphite2-3:amd64. 1502s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 1502s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 1502s Selecting previously unselected package libharfbuzz0b:amd64. 1502s Preparing to unpack .../18-libharfbuzz0b_10.0.1-1_amd64.deb ... 1502s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 1502s Selecting previously unselected package libhtscodecs2:amd64. 1502s Preparing to unpack .../19-libhtscodecs2_1.6.1-1_amd64.deb ... 1502s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 1502s Selecting previously unselected package libhts3t64:amd64. 1502s Preparing to unpack .../20-libhts3t64_1.20+ds-1_amd64.deb ... 1502s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 1502s Selecting previously unselected package libimagequant0:amd64. 1502s Preparing to unpack .../21-libimagequant0_2.18.0-1build1_amd64.deb ... 1502s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 1502s Selecting previously unselected package libjpeg-turbo8:amd64. 1502s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 1502s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 1502s Selecting previously unselected package libjpeg8:amd64. 1502s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_amd64.deb ... 1502s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 1502s Selecting previously unselected package libjs-jquery. 1502s Preparing to unpack .../24-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 1502s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1502s Selecting previously unselected package libjs-jquery-ui. 1502s Preparing to unpack .../25-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 1502s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 1502s Selecting previously unselected package liblapack3:amd64. 1502s Preparing to unpack .../26-liblapack3_3.12.0-3build2_amd64.deb ... 1502s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 1502s Selecting previously unselected package liblbfgsb0:amd64. 1503s Preparing to unpack .../27-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 1503s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1503s Selecting previously unselected package liblcms2-2:amd64. 1503s Preparing to unpack .../28-liblcms2-2_2.16-2_amd64.deb 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python-matplotlib-data. 1503s Preparing to unpack .../39-python-matplotlib-data_3.8.3-3_all.deb ... 1503s Unpacking python-matplotlib-data (3.8.3-3) ... 1503s Selecting previously unselected package python3-appdirs. 1503s Preparing to unpack .../40-python3-appdirs_1.4.4-4_all.deb ... 1503s Unpacking python3-appdirs (1.4.4-4) ... 1503s Selecting previously unselected package python3-six. 1503s Preparing to unpack .../41-python3-six_1.16.0-7_all.deb ... 1503s Unpacking python3-six (1.16.0-7) ... 1503s Selecting previously unselected package python3-dateutil. 1503s Preparing to unpack .../42-python3-dateutil_2.9.0-2_all.deb ... 1503s Unpacking python3-dateutil (2.9.0-2) ... 1503s Selecting previously unselected package libopenjp2-7:amd64. 1503s Preparing to unpack .../43-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 1503s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 1503s Selecting previously unselected package python3-pil:amd64. 1503s Preparing to unpack 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python3-lxml:amd64 (5.3.0-1) ... 1504s Selecting previously unselected package python3-lz4. 1504s Preparing to unpack .../61-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 1504s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 1504s Selecting previously unselected package python3-unicodedata2. 1504s Preparing to unpack .../62-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 1504s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 1504s Selecting previously unselected package unicode-data. 1505s Preparing to unpack .../63-unicode-data_15.1.0-1_all.deb ... 1505s Unpacking unicode-data (15.1.0-1) ... 1505s Selecting previously unselected package python3-fonttools. 1505s Preparing to unpack .../64-python3-fonttools_4.46.0-1build2_amd64.deb ... 1505s Unpacking python3-fonttools (4.46.0-1build2) ... 1505s Selecting previously unselected package python3-kiwisolver. 1505s Preparing to unpack .../65-python3-kiwisolver_1.4.7-2_amd64.deb ... 1505s Unpacking python3-kiwisolver (1.4.7-2) ... 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python3-colorama. 1505s Preparing to unpack .../71-python3-colorama_0.4.6-4_all.deb ... 1505s Unpacking python3-colorama (0.4.6-4) ... 1505s Selecting previously unselected package python3-click. 1505s Preparing to unpack .../72-python3-click_8.1.7-2_all.deb ... 1505s Unpacking python3-click (8.1.7-2) ... 1505s Selecting previously unselected package python3-iniconfig. 1505s Preparing to unpack .../73-python3-iniconfig_1.1.1-2_all.deb ... 1505s Unpacking python3-iniconfig (1.1.1-2) ... 1505s Selecting previously unselected package python3-pysam. 1505s Preparing to unpack .../74-python3-pysam_0.22.1+ds-2_amd64.deb ... 1505s Unpacking python3-pysam (0.22.1+ds-2) ... 1506s Selecting previously unselected package python3-pairtools. 1506s Preparing to unpack .../75-python3-pairtools_1.0.3-1build1_amd64.deb ... 1506s Unpacking python3-pairtools (1.0.3-1build1) ... 1506s Selecting previously unselected package python3-pluggy. 1506s Preparing to unpack .../76-python3-pluggy_1.5.0-1_all.deb ... 1506s Unpacking python3-pluggy (1.5.0-1) ... 1506s Selecting previously unselected package python3-pytest. 1506s Preparing to unpack .../77-python3-pytest_8.3.3-1_all.deb ... 1506s Unpacking python3-pytest (8.3.3-1) ... 1506s Selecting previously unselected package autopkgtest-satdep. 1506s Preparing to unpack .../78-1-autopkgtest-satdep.deb ... 1506s Unpacking autopkgtest-satdep (0) ... 1506s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 1506s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 1506s Setting up liblcms2-2:amd64 (2.16-2) ... 1506s Setting up python3-iniconfig (1.1.1-2) ... 1506s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 1506s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 1506s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 1506s Setting up python3-colorama (0.4.6-4) ... 1506s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 1506s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 1506s Setting up fonts-lyx (2.4.2.1-1) ... 1506s Setting up x11-common (1:7.7+23ubuntu3) ... 1506s Setting up libdeflate0:amd64 (1.22-1) ... 1506s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 1506s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 1506s Setting up python3-click (8.1.7-2) ... 1507s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 1507s Setting up python3-tz (2024.1-2) ... 1507s Setting up unicode-data (15.1.0-1) ... 1507s Setting up python3-six (1.16.0-7) ... 1507s Setting up python3-decorator (5.1.1-5) ... 1507s Setting up libblas3:amd64 (3.12.0-3build2) ... 1507s 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 1507s Setting up python3-packaging (24.1-1) ... 1507s Setting up python3-brotli (1.1.0-2build2) ... 1507s Setting up python3-cycler (0.12.1-1) ... 1507s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 1507s Setting up fonts-dejavu-mono (2.37-8) ... 1507s Setting up python3-kiwisolver (1.4.7-2) ... 1507s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 1507s Setting up fonts-dejavu-core (2.37-8) ... 1507s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 1507s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 1507s Setting up python3-pluggy (1.5.0-1) ... 1507s Setting up libwebp7:amd64 (1.4.0-0.1) ... 1507s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 1507s Setting up libhts3t64:amd64 (1.20+ds-1) ... 1507s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 1507s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 1507s Setting up python3-dateutil (2.9.0-2) ... 1507s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 1507s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 1508s Setting up python3-mpmath (1.3.0-1) ... 1508s Setting up python-matplotlib-data (3.8.3-3) ... 1508s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 1508s Setting up python3-appdirs (1.4.4-4) ... 1508s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 1508s Setting up python3-sympy (1.13.3-1) ... 1513s Setting up liblapack3:amd64 (3.12.0-3build2) ... 1513s 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 1513s Setting up python3-pysam (0.22.1+ds-2) ... 1513s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 1513s Setting up python3-pytest (8.3.3-1) ... 1513s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 1513s Setting up python3-fs (2.4.16-4) ... 1514s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 1514s Setting up libraqm0:amd64 (0.10.1-1build1) ... 1514s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 1515s Setting up python3-lxml:amd64 (5.3.0-1) ... 1515s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 1515s Setting up python3-contourpy (1.3.0-2) ... 1515s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 1515s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 1515s Setting up libxft2:amd64 (2.3.6-1build1) ... 1515s Setting up python3-scipy (1.13.1-5) ... 1518s Setting up libtk8.6:amd64 (8.6.15-1) ... 1518s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 1518s Setting up python3.12-tk (3.12.7-3) ... 1518s Setting up python3.13-tk (3.13.0-2) ... 1518s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 1519s Setting up python3-pandas (2.2.3+dfsg-5) ... 1522s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 1522s Setting up blt (2.5.3+dfsg-7build1) ... 1522s Setting up python3-tk:amd64 (3.12.7-1) ... 1522s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 1522s Setting up python3-fonttools (4.46.0-1build2) ... 1523s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 1523s Setting up python3-matplotlib (3.8.3-3) ... 1524s Setting up python3-bioframe (0.4.1-1) ... 1524s Setting up python3-pairtools (1.0.3-1build1) ... 1524s /usr/lib/python3/dist-packages/pairtools/cli/select.py:90: SyntaxWarning: invalid escape sequence '\d' 1524s """Select pairs according to some condition. 1524s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:928: SyntaxWarning: invalid escape sequence '\w' 1524s """Extract the name of the tile for each read name in the series 1524s Setting up autopkgtest-satdep (0) ... 1524s Processing triggers for libc-bin (2.40-1ubuntu3) ... 1524s Processing triggers for man-db (2.12.1-3) ... 1529s (Reading database ... 84973 files and directories currently installed.) 1529s Removing autopkgtest-satdep (0) ... 1529s autopkgtest [10:13:14]: test upstream-tests: [----------------------- 1529s 1529s rm -rf pairtools 1529s 1529s pytest-3 --ignore=.pc 1530s ============================= test session starts ============================== 1530s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 1530s rootdir: /tmp/autopkgtest.qrAS67/build.a81/src 1530s configfile: pytest.ini 1530s testpaths: tests 1530s plugins: typeguard-4.4.1 1530s collected 31 items 1530s 1533s tests/test_dedup.py . [ 3%] 1535s tests/test_filterbycov.py . [ 6%] 1536s tests/test_flip.py . [ 9%] 1537s tests/test_header.py . [ 12%] 1537s tests/test_headerops.py ....... [ 35%] 1538s tests/test_markasdup.py . [ 38%] 1541s tests/test_merge.py . [ 41%] 1543s tests/test_parse.py ... [ 51%] 1544s tests/test_parse2.py .. [ 58%] 1545s tests/test_restrict.py . [ 61%] 1546s tests/test_scaling.py . [ 64%] 1552s tests/test_select.py ....... [ 87%] 1553s tests/test_sort.py . [ 90%] 1553s tests/test_split.py . [ 93%] 1558s tests/test_stats.py .. [100%] 1558s 1558s =============================== warnings summary =============================== 1558s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 1558s /usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 1558s import pipes 1558s 1558s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1558s ======================== 31 passed, 1 warning in 28.66s ======================== 1558s ALL PASS 1558s 1558s echo ALL PASS 1559s autopkgtest [10:13:44]: test upstream-tests: -----------------------] 1559s autopkgtest [10:13:44]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 1559s upstream-tests PASS 1560s autopkgtest [10:13:45]: @@@@@@@@@@@@@@@@@@@@ summary 1560s upstream-tests PASS 1728s nova [W] Skipping flock for amd64 1728s Creating nova instance adt-plucky-amd64-pairtools-20241113-091106-juju-7f2275-prod-proposed-migration-environment-20-4689d2f9-778b-4bd0-9428-61299f0c6c0c from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)... 1728s nova [W] nova quota exceeded (attempt #0)