0s autopkgtest [21:30:36]: starting date and time: 2025-02-15 21:30:36+0000 0s autopkgtest [21:30:36]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:30:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vac3ppso/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade pairtools --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@lcy02-5.secgroup --name adt-plucky-amd64-pairtools-20250215-213036-juju-7f2275-prod-proposed-migration-environment-20-8444d7c2-718b-45dc-baf4-0279d1ffa5eb --image adt/ubuntu-plucky-amd64-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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 52s autopkgtest [21:31:28]: testbed dpkg architecture: amd64 52s autopkgtest [21:31:28]: testbed apt version: 2.9.28 52s autopkgtest [21:31:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 52s autopkgtest [21:31:28]: testbed release detected to be: None 53s autopkgtest [21:31:28]: updating testbed package index (apt update) 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 53s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 53s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 53s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 53s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 53s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [820 kB] 53s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 53s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB] 53s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 53s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 53s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [844 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [303 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 53s Fetched 2329 kB in 1s (3709 kB/s) 55s Reading package lists... 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s The following packages will be upgraded: 56s dash libtasn1-6 libxdmcp6 57s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 168 kB of archives. 57s After this operation, 56.3 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 dash amd64 0.5.12-12ubuntu1 [105 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [11.0 kB] 58s Preconfiguring packages ... 58s Fetched 168 kB in 0s (3041 kB/s) 58s (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 ... 108914 files and directories currently installed.) 58s Preparing to unpack .../dash_0.5.12-12ubuntu1_amd64.deb ... 58s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 58s Setting up dash (0.5.12-12ubuntu1) ... 58s (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 ... 108914 files and directories currently installed.) 58s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 58s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 58s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_amd64.deb ... 58s Unpacking libxdmcp6:amd64 (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 58s Setting up libxdmcp6:amd64 (1:1.1.5-1) ... 58s Setting up libtasn1-6:amd64 (4.20.0-2) ... 58s Processing triggers for libc-bin (2.40-4ubuntu1) ... 58s Processing triggers for man-db (2.13.0-1) ... 59s Processing triggers for debianutils (5.21) ... 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 60s autopkgtest [21:31:36]: upgrading testbed (apt dist-upgrade and autopurge) 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 62s Entering ResolveByKeep 63s 63s The following packages will be upgraded: 63s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 63s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 11.8 MB of archives. 63s After this operation, 746 kB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 64s Preconfiguring packages ... 64s Fetched 11.8 MB in 0s (26.1 MB/s) 64s (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 ... 108914 files and directories currently installed.) 64s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 64s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 64s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 64s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 65s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 65s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 65s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 65s Checking for services that may need to be restarted... 65s Checking init scripts... 65s Checking for services that may need to be restarted... 65s Checking init scripts... 65s Stopping some services possibly affected by the upgrade (will be restarted later): 65s cron: stopping...done. 65s 65s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 66s Setting up libc6:amd64 (2.41-1ubuntu1) ... 66s Checking for services that may need to be restarted... 66s Checking init scripts... 66s Restarting services possibly affected by the upgrade: 66s cron: restarting...done. 66s 66s Services restarted successfully. 66s (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 ... 108915 files and directories currently installed.) 66s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 66s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 66s Setting up libc-bin (2.41-1ubuntu1) ... 66s (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 ... 108915 files and directories currently installed.) 66s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 66s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 67s Setting up iproute2 (6.13.0-1ubuntu1) ... 67s Setting up locales (2.41-1ubuntu1) ... 67s Installing new version of config file /etc/locale.alias ... 68s Generating locales (this might take a while)... 69s en_US.UTF-8... done 69s Generation complete. 70s Setting up libc-dev-bin (2.41-1ubuntu1) ... 70s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 70s Processing triggers for man-db (2.13.0-1) ... 71s Processing triggers for systemd (257.2-3ubuntu1) ... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Starting pkgProblemResolver with broken count: 0 72s Starting 2 pkgProblemResolver with broken count: 0 72s Done 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [21:31:50]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 75s autopkgtest [21:31:51]: @@@@@@@@@@@@@@@@@@@@ apt-source pairtools 76s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.1.2-1 (dsc) [2470 B] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.1.2-1 (tar) [1419 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pairtools 1.1.2-1 (diff) [7580 B] 76s gpgv: Signature made Sat Dec 21 20:37:34 2024 UTC 76s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 76s gpgv: issuer "tchet@debian.org" 76s gpgv: Can't check signature: No public key 76s dpkg-source: warning: cannot verify inline signature for ./pairtools_1.1.2-1.dsc: no acceptable signature found 76s autopkgtest [21:31:52]: testing package pairtools version 1.1.2-1 78s autopkgtest [21:31:54]: build not needed 78s autopkgtest [21:31:54]: test upstream-tests: preparing testbed 78s Reading package lists... 78s Building dependency tree... 78s Reading state information... 79s Starting pkgProblemResolver with broken count: 0 79s Starting 2 pkgProblemResolver with broken count: 0 79s Done 80s The following NEW packages will be installed: 80s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3 80s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 80s libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0 libjbig0 80s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 80s liblcms2-2 liblerc4 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 80s libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxft2 80s libxrender1 libxslt1.1 libxss1 python-is-python3 python-matplotlib-data 80s python3-bioframe python3-brotli python3-click python3-contourpy 80s python3-cycler python3-dateutil python3-decorator python3-fonttools 80s python3-fs python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 80s python3-matplotlib python3-mpmath python3-numpy python3-packaging 80s python3-pairtools python3-pandas python3-pandas-lib python3-pil 80s python3-pil.imagetk python3-platformdirs python3-pluggy python3-pysam 80s python3-pytest python3-pytz python3-scipy python3-standard-pipes 80s python3-sympy python3-tk python3-tz python3-ufolib2 python3-unicodedata2 80s python3.12-tk python3.13-tk tk8.6-blt2.5 unicode-data x11-common 80s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 84.3 MB of archives. 80s After this operation, 447 MB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 80s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 80s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 80s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 80s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 80s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 80s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 80s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 80s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 80s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 80s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 80s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 80s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 80s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 80s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 80s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 80s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 80s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 80s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 80s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 80s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 80s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 80s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 80s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 80s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 80s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 80s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 80s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 80s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 80s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 80s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 80s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 80s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 80s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 80s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 80s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 80s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 80s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 80s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 80s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python-is-python3 all 3.11.4-1 [2684 B] 80s Get:41 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3ubuntu2 [2929 kB] 80s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 80s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 80s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 80s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 80s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-1 [107 kB] 80s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 80s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5 [9936 B] 80s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 80s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1 [271 kB] 80s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 80s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build3 [368 kB] 80s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 80s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 80s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 80s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-6 [90.7 kB] 80s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1 [1831 kB] 80s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1 [27.4 kB] 80s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 80s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 80s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 80s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 80s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 80s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build2 [360 kB] 80s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 80s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2 [1755 kB] 80s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3 [70.4 kB] 80s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 80s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3ubuntu2 [4697 kB] 80s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 80s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 80s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-bioframe all 0.4.1-1 [76.1 kB] 80s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.8-1 [79.8 kB] 80s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 80s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-standard-pipes all 3.13.0-5 [7414 B] 80s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1 [4558 kB] 80s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pairtools amd64 1.1.2-1 [309 kB] 80s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 80s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.4-1 [252 kB] 81s Fetched 84.3 MB in 1s (110 MB/s) 81s Selecting previously unselected package libtcl8.6:amd64. 81s (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 ... 108916 files and directories currently installed.) 81s Preparing to unpack .../00-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 81s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 81s Selecting previously unselected package fonts-dejavu-mono. 81s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 81s Unpacking fonts-dejavu-mono (2.37-8) ... 81s Selecting previously unselected package fonts-dejavu-core. 81s Preparing to unpack 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liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 83s Selecting previously unselected package libqhull-r8.0:amd64. 83s Preparing to unpack .../30-libqhull-r8.0_2020.2-6build1_amd64.deb ... 83s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 83s Selecting previously unselected package libraqm0:amd64. 83s Preparing to unpack .../31-libraqm0_0.10.2-1_amd64.deb ... 83s Unpacking libraqm0:amd64 (0.10.2-1) ... 83s Selecting previously unselected package libsharpyuv0:amd64. 83s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_amd64.deb ... 83s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 83s Selecting previously unselected package libjbig0:amd64. 83s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 83s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 83s Selecting previously unselected package libwebp7:amd64. 83s Preparing to unpack .../34-libwebp7_1.5.0-0.1_amd64.deb ... 83s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 83s Selecting previously unselected package libtiff6:amd64. 83s 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python3-lz4. 85s Preparing to unpack .../57-python3-lz4_4.4.0+dfsg-1_amd64.deb ... 85s Unpacking python3-lz4 (4.4.0+dfsg-1) ... 85s Selecting previously unselected package python3-decorator. 85s Preparing to unpack .../58-python3-decorator_5.1.1-5_all.deb ... 85s Unpacking python3-decorator (5.1.1-5) ... 85s Selecting previously unselected package python3-scipy. 85s Preparing to unpack .../59-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 85s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 86s Selecting previously unselected package python3-mpmath. 86s Preparing to unpack .../60-python3-mpmath_1.3.0-1_all.deb ... 86s Unpacking python3-mpmath (1.3.0-1) ... 86s Selecting previously unselected package python3-sympy. 86s Preparing to unpack .../61-python3-sympy_1.13.3-1_all.deb ... 86s Unpacking python3-sympy (1.13.3-1) ... 86s Selecting previously unselected package python3-ufolib2. 86s Preparing to unpack .../62-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 86s Unpacking python3-ufolib2 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Unpacking python3-iniconfig (1.1.1-2) ... 88s Selecting previously unselected package python3-standard-pipes. 88s Preparing to unpack .../74-python3-standard-pipes_3.13.0-5_all.deb ... 88s Unpacking python3-standard-pipes (3.13.0-5) ... 88s Selecting previously unselected package python3-pysam. 88s Preparing to unpack .../75-python3-pysam_0.23.0+ds-1_amd64.deb ... 88s Unpacking python3-pysam (0.23.0+ds-1) ... 88s Selecting previously unselected package python3-pairtools. 88s Preparing to unpack .../76-python3-pairtools_1.1.2-1_amd64.deb ... 88s Unpacking python3-pairtools (1.1.2-1) ... 88s Selecting previously unselected package python3-pluggy. 88s Preparing to unpack .../77-python3-pluggy_1.5.0-1_all.deb ... 88s Unpacking python3-pluggy (1.5.0-1) ... 88s Selecting previously unselected package python3-pytest. 88s Preparing to unpack .../78-python3-pytest_8.3.4-1_all.deb ... 88s Unpacking python3-pytest (8.3.4-1) ... 88s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 88s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 88s Setting up liblcms2-2:amd64 (2.16-2) ... 88s Setting up python3-iniconfig (1.1.1-2) ... 88s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 88s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 88s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 88s Setting up python3-standard-pipes (3.13.0-5) ... 88s Setting up python3-lz4 (4.4.0+dfsg-1) ... 89s Setting up python3-unicodedata2 (15.1.0+ds-1build2) ... 89s Setting up fonts-lyx (2.4.3-1) ... 89s Setting up x11-common (1:7.7+23ubuntu3) ... 89s Setting up libdeflate0:amd64 (1.23-1) ... 89s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 89s Setting up python3-pytz (2025.1-3) ... 89s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ... 89s Setting up python3-click (8.1.8-1) ... 90s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 90s Setting up python3-platformdirs (4.3.6-1) ... 90s Setting up python3-tz (2025.1-3) ... 90s Setting up python3-fs (2.4.16-6) ... 90s Setting up unicode-data (15.1.0-1) ... 90s Setting up python3-decorator (5.1.1-5) ... 90s Setting up libblas3:amd64 (3.12.1-2) ... 90s 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 90s Setting up python3-packaging (24.2-1) ... 90s Setting up python3-brotli (1.1.0-2build3) ... 90s Setting up python3-cycler (0.12.1-1) ... 91s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 91s Setting up fonts-dejavu-mono (2.37-8) ... 91s Setting up python3-kiwisolver (1.4.7-3) ... 91s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 91s Setting up fonts-dejavu-core (2.37-8) ... 91s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 91s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ... 91s Setting up python3-pluggy (1.5.0-1) ... 91s Setting up libwebp7:amd64 (1.5.0-0.1) ... 91s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 91s Setting up libhts3t64:amd64 (1.21+ds-1) ... 91s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 91s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 91s Setting up python3-dateutil (2.9.0-3) ... 91s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 91s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 91s Setting up python3-mpmath (1.3.0-1) ... 92s Setting up python-matplotlib-data (3.8.3-3ubuntu2) ... 92s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 92s Setting up python-is-python3 (3.11.4-1) ... 92s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 92s Setting up python3-sympy (1.13.3-1) ... 99s Setting up liblapack3:amd64 (3.12.1-2) ... 99s 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 99s Setting up python3-pysam (0.23.0+ds-1) ... 100s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 100s Setting up python3-pytest (8.3.4-1) ... 100s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 100s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 100s Setting up libraqm0:amd64 (0.10.2-1) ... 100s Setting up python3-numpy (1:1.26.4+ds-13) ... 102s Setting up python3-lxml:amd64 (5.3.1-1) ... 102s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 102s Setting up python3-contourpy (1.3.1-1) ... 102s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 102s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 102s Setting up libxft2:amd64 (2.3.6-1build1) ... 102s Setting up python3-scipy (1.14.1-4ubuntu1) ... 106s Setting up libtk8.6:amd64 (8.6.16-1) ... 106s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 106s Setting up python3.12-tk (3.12.9-1) ... 106s Setting up python3.13-tk (3.13.2-1) ... 106s Setting up python3-pil:amd64 (11.1.0-5) ... 106s Setting up python3-pandas (2.2.3+dfsg-8) ... 111s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 111s Setting up blt (2.5.3+dfsg-7build1) ... 111s Setting up python3-tk:amd64 (3.13.1-1) ... 111s Setting up python3-pil.imagetk:amd64 (11.1.0-5) ... 111s Setting up python3-fonttools (4.55.3-2) ... 112s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 112s Setting up python3-matplotlib (3.8.3-3ubuntu2) ... 114s Setting up python3-bioframe (0.4.1-1) ... 114s Setting up python3-pairtools (1.1.2-1) ... 114s Processing triggers for libc-bin (2.41-1ubuntu1) ... 114s Processing triggers for man-db (2.13.0-1) ... 116s autopkgtest [21:32:32]: test upstream-tests: [----------------------- 116s 116s rm -rf pairtools 116s 116s pytest-3 --ignore=.pc 117s ============================= test session starts ============================== 117s platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 117s rootdir: /tmp/autopkgtest.gXAbxp/build.Zzv/src 117s configfile: pytest.ini 117s testpaths: tests 117s plugins: typeguard-4.4.1 117s collected 34 items 117s 124s tests/test_dedup.py . [ 2%] 128s tests/test_filterbycov.py . [ 5%] 129s tests/test_flip.py . [ 8%] 131s tests/test_header.py . [ 11%] 131s tests/test_headerops.py ....... [ 32%] 132s tests/test_markasdup.py . [ 35%] 138s tests/test_merge.py . [ 38%] 141s tests/test_parse.py ... [ 47%] 146s tests/test_parse2.py .... [ 58%] 148s tests/test_restrict.py . [ 61%] 149s tests/test_scaling.py . [ 64%] 159s tests/test_select.py ....... [ 85%] 160s tests/test_sort.py . [ 88%] 161s tests/test_split.py . [ 91%] 170s tests/test_stats.py ... [100%] 170s 170s =============================== warnings summary =============================== 170s ../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2 170s /usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2: DeprecationWarning: pipes was removed in Python 3.13. Please be aware that you are currently NOT using standard 'pipes', but instead a separately installed 'standard-pipes'. 170s import pipes 170s 170s tests/test_stats.py::test_find_dist_freq_convergence_distance 170s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: divide by zero encountered in scalar divide 170s strands: n_cis_pairs / norm_factor 170s 170s tests/test_stats.py::test_find_dist_freq_convergence_distance 170s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: divide by zero encountered in scalar divide 170s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 170s 170s tests/test_stats.py::test_find_dist_freq_convergence_distance 170s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:410: RuntimeWarning: invalid value encountered in divide 170s np.abs(dist_freqs_by_strands[strands] - avg_freq_all_strands) 170s 170s tests/test_stats.py::test_find_dist_freq_convergence_distance 170s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: invalid value encountered in scalar divide 170s strands: n_cis_pairs / norm_factor 170s 170s tests/test_stats.py::test_find_dist_freq_convergence_distance 170s /usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: invalid value encountered in scalar divide 170s sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor ) 170s 170s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 170s ======================= 34 passed, 6 warnings in 54.05s ======================== 170s ALL PASS 170s 170s echo ALL PASS 171s autopkgtest [21:33:27]: test upstream-tests: -----------------------] 171s upstream-tests PASS 171s autopkgtest [21:33:27]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - - 171s autopkgtest [21:33:27]: @@@@@@@@@@@@@@@@@@@@ summary 171s upstream-tests PASS 187s nova [W] Skipping flock for amd64 187s Creating nova instance adt-plucky-amd64-pairtools-20250215-213036-juju-7f2275-prod-proposed-migration-environment-20-8444d7c2-718b-45dc-baf4-0279d1ffa5eb from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID 5f605d3a-6e26-4e15-b556-0020b04f5a0d)... 187s nova [W] Timed out waiting for 475cfd7a-8f7a-48d4-9d5a-5178a5f0e1ef to get deleted.