0s autopkgtest [01:17:50]: starting date and time: 2025-03-08 01:17:50+0000 0s autopkgtest [01:17:50]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:17:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.r6m6ih1i/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-stdlib-extensions --apt-upgrade ariba --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-stdlib-extensions/3.13.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-13.secgroup --name adt-plucky-ppc64el-ariba-20250308-011750-juju-7f2275-prod-proposed-migration-environment-2-3116446e-28d2-4bfd-8c82-a1e0dd25be9f --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -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/ 107s autopkgtest [01:19:37]: testbed dpkg architecture: ppc64el 107s autopkgtest [01:19:37]: testbed apt version: 2.9.31ubuntu1 108s autopkgtest [01:19:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 108s autopkgtest [01:19:38]: testbed release detected to be: None 109s autopkgtest [01:19:39]: updating testbed package index (apt update) 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 109s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 109s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [11.5 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [6640 B] 109s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [47.3 kB] 109s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [390 kB] 110s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [71.4 kB] 110s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [266 kB] 110s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [3012 B] 110s Fetched 906 kB in 1s (1092 kB/s) 110s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade... 112s Calculating upgrade... 112s The following packages will be upgraded: 112s gir1.2-girepository-2.0 libgirepository-1.0-1 libjemalloc2 liblzma5 xz-utils 112s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 832 kB of archives. 112s After this operation, 17.4 kB of additional disk space will be used. 112s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblzma5 ppc64el 5.6.4-1 [173 kB] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgirepository-1.0-1 ppc64el 1.83.2-1 [96.3 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el gir1.2-girepository-2.0 ppc64el 1.83.2-1 [25.3 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el xz-utils ppc64el 5.6.4-1 [282 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjemalloc2 ppc64el 5.3.0-3 [256 kB] 113s Fetched 832 kB in 1s (1379 kB/s) 113s (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 ... 106518 files and directories currently installed.) 113s Preparing to unpack .../liblzma5_5.6.4-1_ppc64el.deb ... 113s Unpacking liblzma5:ppc64el (5.6.4-1) over (5.6.3-1) ... 113s Setting up liblzma5:ppc64el (5.6.4-1) ... 113s (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 ... 106518 files and directories currently installed.) 113s Preparing to unpack .../libgirepository-1.0-1_1.83.2-1_ppc64el.deb ... 113s Unpacking libgirepository-1.0-1:ppc64el (1.83.2-1) over (1.82.0-4) ... 113s Preparing to unpack .../gir1.2-girepository-2.0_1.83.2-1_ppc64el.deb ... 113s Unpacking gir1.2-girepository-2.0:ppc64el (1.83.2-1) over (1.82.0-4) ... 113s Preparing to unpack .../xz-utils_5.6.4-1_ppc64el.deb ... 113s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 113s Preparing to unpack .../libjemalloc2_5.3.0-3_ppc64el.deb ... 113s Unpacking libjemalloc2:ppc64el (5.3.0-3) over (5.3.0-2build1) ... 113s Setting up libjemalloc2:ppc64el (5.3.0-3) ... 113s Setting up xz-utils (5.6.4-1) ... 113s Setting up libgirepository-1.0-1:ppc64el (1.83.2-1) ... 113s Setting up gir1.2-girepository-2.0:ppc64el (1.83.2-1) ... 113s Processing triggers for man-db (2.13.0-1) ... 114s Processing triggers for libc-bin (2.41-1ubuntu1) ... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Solving dependencies... 114s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 114s autopkgtest [01:19:44]: upgrading testbed (apt dist-upgrade and autopurge) 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 115s Entering ResolveByKeep 115s 116s Calculating upgrade... 116s The following package was automatically installed and is no longer required: 116s python3.12-gdbm 116s Use 'sudo apt autoremove' to remove it. 116s The following packages will be upgraded: 116s python3-gdbm 116s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 8708 B of archives. 116s After this operation, 0 B of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.13.2-1 [8708 B] 116s Fetched 8708 B in 0s (62.7 kB/s) 116s (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 ... 106518 files and directories currently installed.) 116s Preparing to unpack .../python3-gdbm_3.13.2-1_ppc64el.deb ... 116s Unpacking python3-gdbm:ppc64el (3.13.2-1) over (3.13.1-1) ... 116s Setting up python3-gdbm:ppc64el (3.13.2-1) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 117s Solving dependencies... 117s The following packages will be REMOVED: 117s python3.12-gdbm* 117s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 117s After this operation, 140 kB disk space will be freed. 117s (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 ... 106518 files and directories currently installed.) 117s Removing python3.12-gdbm (3.12.9-1) ... 120s autopkgtest [01:19:50]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP Fri Feb 14 16:16:28 UTC 2025 120s autopkgtest [01:19:50]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 122s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (dsc) [2435 B] 122s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (tar) [1920 kB] 122s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (diff) [11.5 kB] 122s gpgv: Signature made Thu Jan 30 21:44:32 2025 UTC 122s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 122s gpgv: issuer "emollier@debian.org" 122s gpgv: Can't check signature: No public key 122s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7.dsc: no acceptable signature found 122s autopkgtest [01:19:52]: testing package ariba version 2.14.7+ds-7 122s autopkgtest [01:19:52]: build not needed 124s autopkgtest [01:19:54]: test test-example: preparing testbed 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Starting pkgProblemResolver with broken count: 0 124s Starting 2 pkgProblemResolver with broken count: 0 124s Done 124s The following NEW packages will be installed: 124s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 124s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 124s libcapnp-1.1.0 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 124s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 124s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 124s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 124s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 124s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 124s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 124s mummer python-matplotlib-data python3-biopython python3-brotli python3-bs4 124s python3-cairo python3-contourpy python3-cycler python3-dateutil 124s python3-decorator python3-dendropy python3-fonttools python3-freetype 124s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 124s python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil 124s python3-pil.imagetk python3-platformdirs python3-pymummer python3-pysam 124s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 124s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3.13-tk 124s samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 124s xfonts-encodings xfonts-utils xml-core 125s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 109 MB of archives. 125s After this operation, 494 MB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy-dev ppc64el 1:2.2.3+ds-4 [154 kB] 125s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.1-2 [239 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250222-0ubuntu1 [612 kB] 125s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.1-2 [2813 kB] 125s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:2.2.3+ds-4 [4836 kB] 125s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 125s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.23-1 [63.4 kB] 125s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-2 [113 kB] 125s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.21+ds-1 [585 kB] 125s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el samtools ppc64el 1.21-1 [690 kB] 125s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fastaq all 3.17.0-9 [48.2 kB] 125s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.16+dfsg-1 [1201 kB] 125s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 125s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 125s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 125s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 125s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 125s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 125s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 126s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-2ubuntu1 [37.5 kB] 126s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-2ubuntu1 [188 kB] 126s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 126s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 126s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 126s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.16-1 [946 kB] 126s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-tk ppc64el 3.13.2-1 [107 kB] 126s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-8 [778 kB] 126s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-8 [4830 B] 126s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-tk ppc64el 3.13.2-1 [9818 B] 126s Get:30 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 11.1.0-5build1 [10.3 kB] 126s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 15-20250222-0ubuntu1 [168 kB] 126s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 126s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB] 126s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 126s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 126s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu3 [247 kB] 126s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 126s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.2.0-1 [598 kB] 126s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.2-1 [19.2 kB] 126s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 126s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 126s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 126s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 126s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 126s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.5.0-0.1 [14.6 kB] 126s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.5.0-0.1 [31.1 kB] 126s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 11.1.0-5build1 [601 kB] 126s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 126s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 126s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 126s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 126s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2build2 [129 kB] 126s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 126s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 126s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.3.1-1 [1137 kB] 126s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 126s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 126s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.85+dfsg-2build1 [1766 kB] 126s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-soupsieve all 2.6-1 [33.0 kB] 126s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bs4 all 4.13.3-1 [136 kB] 126s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-dendropy all 4.6.1-2 [278 kB] 126s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 126s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 126s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.3-1 [171 kB] 126s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-7build1 [2934 kB] 126s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 126s Get:67 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.1-1build1 [218 kB] 126s Get:68 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 126s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build4 [422 kB] 126s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-platformdirs all 4.3.6-1 [16.8 kB] 126s Get:71 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-7 [90.8 kB] 126s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu2 [191 kB] 126s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.1-1build1 [1393 kB] 126s Get:74 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.4.0+dfsg-1build1 [28.1 kB] 126s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 126s Get:76 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 126s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.14.1-4ubuntu1 [22.7 MB] 127s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 127s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-5 [4229 kB] 127s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 127s Get:81 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build3 [361 kB] 127s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 127s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.55.3-2build1 [1521 kB] 127s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-3build1 [59.5 kB] 127s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.2-1 [51.5 kB] 127s Get:86 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 127s Get:87 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-7build1 [17.4 MB] 128s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mummer ppc64el 3.23+dfsg-8 [714 kB] 128s Get:89 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pymummer all 0.11.0-5 [17.3 kB] 128s Get:90 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.23.0+ds-1build1 [4039 kB] 128s Get:91 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libfml0 ppc64el 0.1+git20221215.85f159e-1 [87.9 kB] 128s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libminimap0 ppc64el 0.2-8 [26.3 kB] 128s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el bowtie2 ppc64el 2.5.4-1 [1437 kB] 128s Get:94 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cd-hit ppc64el 4.8.1-4 [547 kB] 128s Get:95 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libcapnp-1.1.0 ppc64el 1.1.0-2 [1576 kB] 128s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgslcblas0 ppc64el 2.8+dfsg-5 [276 kB] 128s Get:97 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libgsl28 ppc64el 2.8+dfsg-5 [1394 kB] 128s Get:98 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libmurmurhash2 ppc64el 1.6-1 [6626 B] 128s Get:99 http://ftpmaster.internal/ubuntu plucky/universe ppc64el mash ppc64el 2.3+dfsg-6build2 [163 kB] 128s Get:100 http://ftpmaster.internal/ubuntu plucky/universe ppc64el ariba ppc64el 2.14.7+ds-7 [2034 kB] 128s Fetched 109 MB in 3s (32.8 MB/s) 128s Selecting previously unselected package python3-numpy-dev:ppc64el. 128s (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 ... 106513 files and directories currently installed.) 128s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-4_ppc64el.deb ... 128s Unpacking python3-numpy-dev:ppc64el (1:2.2.3+ds-4) ... 128s Selecting previously unselected package libblas3:ppc64el. 128s Preparing to unpack .../01-libblas3_3.12.1-2_ppc64el.deb ... 128s Unpacking libblas3:ppc64el (3.12.1-2) ... 128s Selecting previously unselected package libgfortran5:ppc64el. 128s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_ppc64el.deb ... 128s Unpacking libgfortran5:ppc64el (15-20250222-0ubuntu1) ... 128s Selecting previously unselected package liblapack3:ppc64el. 128s Preparing to unpack .../03-liblapack3_3.12.1-2_ppc64el.deb ... 128s Unpacking liblapack3:ppc64el (3.12.1-2) ... 128s Selecting previously unselected package python3-numpy. 128s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-4_ppc64el.deb ... 128s Unpacking python3-numpy (1:2.2.3+ds-4) ... 129s Selecting previously unselected package sgml-base. 129s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 129s Unpacking sgml-base (1.31) ... 129s Selecting previously unselected package libdeflate0:ppc64el. 129s Preparing to unpack .../06-libdeflate0_1.23-1_ppc64el.deb ... 129s Unpacking libdeflate0:ppc64el (1.23-1) ... 129s Selecting previously unselected package libhtscodecs2:ppc64el. 129s Preparing to unpack .../07-libhtscodecs2_1.6.1-2_ppc64el.deb ... 129s Unpacking libhtscodecs2:ppc64el (1.6.1-2) ... 129s Selecting previously unselected package libhts3t64:ppc64el. 129s Preparing to unpack .../08-libhts3t64_1.21+ds-1_ppc64el.deb ... 129s Unpacking libhts3t64:ppc64el (1.21+ds-1) ... 129s Selecting previously unselected package samtools. 129s Preparing to unpack .../09-samtools_1.21-1_ppc64el.deb ... 129s Unpacking samtools (1.21-1) ... 129s Selecting previously unselected package fastaq. 129s Preparing to unpack .../10-fastaq_3.17.0-9_all.deb ... 129s Unpacking fastaq (3.17.0-9) ... 129s Selecting previously unselected package libtcl8.6:ppc64el. 129s Preparing to unpack .../11-libtcl8.6_8.6.16+dfsg-1_ppc64el.deb ... 129s Unpacking libtcl8.6:ppc64el (8.6.16+dfsg-1) ... 129s Selecting previously unselected package fonts-dejavu-mono. 129s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 129s Unpacking fonts-dejavu-mono (2.37-8) ... 129s Selecting previously unselected package fonts-dejavu-core. 129s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 129s Unpacking fonts-dejavu-core (2.37-8) ... 129s Selecting previously unselected package libfontenc1:ppc64el. 129s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 129s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 129s Selecting previously unselected package x11-common. 129s Preparing to unpack .../15-x11-common_1%3a7.7+23ubuntu3_all.deb ... 129s Unpacking x11-common (1:7.7+23ubuntu3) ... 129s Selecting previously unselected package xfonts-encodings. 129s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 129s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 129s Selecting previously unselected package xfonts-utils. 129s Preparing to unpack .../17-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 129s Unpacking xfonts-utils (1:7.7+7) ... 129s Selecting previously unselected package fonts-urw-base35. 129s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 129s Unpacking fonts-urw-base35 (20200910-8) ... 129s Selecting previously unselected package fontconfig-config. 129s Preparing to unpack .../19-fontconfig-config_2.15.0-2ubuntu1_ppc64el.deb ... 129s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 129s Selecting previously unselected package libfontconfig1:ppc64el. 129s Preparing to unpack .../20-libfontconfig1_2.15.0-2ubuntu1_ppc64el.deb ... 129s Unpacking libfontconfig1:ppc64el (2.15.0-2ubuntu1) ... 129s Selecting previously unselected package libxrender1:ppc64el. 129s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 129s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 129s Selecting previously unselected package libxft2:ppc64el. 129s Preparing to unpack .../22-libxft2_2.3.6-1build1_ppc64el.deb ... 129s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 129s Selecting previously unselected package libxss1:ppc64el. 129s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 129s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 129s Selecting previously unselected package libtk8.6:ppc64el. 129s Preparing to unpack .../24-libtk8.6_8.6.16-1_ppc64el.deb ... 129s Unpacking libtk8.6:ppc64el (8.6.16-1) ... 129s Selecting previously unselected package python3.13-tk. 129s Preparing to unpack .../25-python3.13-tk_3.13.2-1_ppc64el.deb ... 129s Unpacking python3.13-tk (3.13.2-1) ... 129s Selecting previously unselected package tk8.6-blt2.5. 129s Preparing to unpack .../26-tk8.6-blt2.5_2.5.3+dfsg-8_ppc64el.deb ... 129s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 129s Selecting previously unselected package blt. 129s Preparing to unpack .../27-blt_2.5.3+dfsg-8_ppc64el.deb ... 129s Unpacking blt (2.5.3+dfsg-8) ... 129s Selecting previously unselected package python3-tk:ppc64el. 129s Preparing to unpack .../28-python3-tk_3.13.2-1_ppc64el.deb ... 129s Unpacking python3-tk:ppc64el (3.13.2-1) ... 129s Selecting previously unselected package python3-pil.imagetk:ppc64el. 129s Preparing to unpack .../29-python3-pil.imagetk_11.1.0-5build1_ppc64el.deb ... 129s Unpacking python3-pil.imagetk:ppc64el (11.1.0-5build1) ... 129s Selecting previously unselected package libgomp1:ppc64el. 129s Preparing to unpack .../30-libgomp1_15-20250222-0ubuntu1_ppc64el.deb ... 129s Unpacking libgomp1:ppc64el (15-20250222-0ubuntu1) ... 129s Selecting previously unselected package libimagequant0:ppc64el. 129s Preparing to unpack .../31-libimagequant0_2.18.0-1build1_ppc64el.deb ... 129s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 129s Selecting previously unselected package libjpeg-turbo8:ppc64el. 129s Preparing to unpack .../32-libjpeg-turbo8_2.1.5-3ubuntu2_ppc64el.deb ... 129s Unpacking libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ... 129s Selecting previously unselected package libjpeg8:ppc64el. 129s Preparing to unpack .../33-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 129s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 129s Selecting previously unselected package liblcms2-2:ppc64el. 129s Preparing to unpack .../34-liblcms2-2_2.16-2_ppc64el.deb ... 129s Unpacking liblcms2-2:ppc64el (2.16-2) ... 129s Selecting previously unselected package libopenjp2-7:ppc64el. 129s Preparing to unpack .../35-libopenjp2-7_2.5.0-2ubuntu3_ppc64el.deb ... 129s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu3) ... 130s Selecting previously unselected package libgraphite2-3:ppc64el. 130s Preparing to unpack .../36-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 130s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 130s Selecting previously unselected package libharfbuzz0b:ppc64el. 130s Preparing to unpack .../37-libharfbuzz0b_10.2.0-1_ppc64el.deb ... 130s Unpacking libharfbuzz0b:ppc64el (10.2.0-1) ... 130s Selecting previously unselected package libraqm0:ppc64el. 130s Preparing to unpack .../38-libraqm0_0.10.2-1_ppc64el.deb ... 130s Unpacking libraqm0:ppc64el (0.10.2-1) ... 130s Selecting previously unselected package libjbig0:ppc64el. 130s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 130s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 130s Selecting previously unselected package liblerc4:ppc64el. 130s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_ppc64el.deb ... 130s Unpacking liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 130s Selecting previously unselected package libsharpyuv0:ppc64el. 130s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_ppc64el.deb ... 130s Unpacking libsharpyuv0:ppc64el (1.5.0-0.1) ... 130s Selecting previously unselected package libwebp7:ppc64el. 130s Preparing to unpack .../42-libwebp7_1.5.0-0.1_ppc64el.deb ... 130s Unpacking libwebp7:ppc64el (1.5.0-0.1) ... 130s Selecting previously unselected package libtiff6:ppc64el. 130s Preparing to unpack .../43-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 130s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 130s Selecting previously unselected package libwebpdemux2:ppc64el. 130s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_ppc64el.deb ... 130s Unpacking libwebpdemux2:ppc64el (1.5.0-0.1) ... 130s Selecting previously unselected package libwebpmux3:ppc64el. 130s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_ppc64el.deb ... 130s Unpacking libwebpmux3:ppc64el (1.5.0-0.1) ... 130s Selecting previously unselected package python3-pil:ppc64el. 130s Preparing to unpack .../46-python3-pil_11.1.0-5build1_ppc64el.deb ... 130s Unpacking python3-pil:ppc64el (11.1.0-5build1) ... 130s Selecting previously unselected package libpixman-1-0:ppc64el. 130s Preparing to unpack .../47-libpixman-1-0_0.44.0-3_ppc64el.deb ... 130s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 130s Selecting previously unselected package libxcb-render0:ppc64el. 130s Preparing to unpack .../48-libxcb-render0_1.17.0-2_ppc64el.deb ... 130s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 130s Selecting previously unselected package libxcb-shm0:ppc64el. 130s Preparing to unpack .../49-libxcb-shm0_1.17.0-2_ppc64el.deb ... 130s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 130s Selecting previously unselected package libcairo2:ppc64el. 130s Preparing to unpack .../50-libcairo2_1.18.2-2_ppc64el.deb ... 130s Unpacking libcairo2:ppc64el (1.18.2-2) ... 130s Selecting previously unselected package python3-cairo. 130s Preparing to unpack .../51-python3-cairo_1.26.1-2build2_ppc64el.deb ... 130s Unpacking python3-cairo (1.26.1-2build2) ... 130s Selecting previously unselected package python3-freetype. 130s Preparing to unpack .../52-python3-freetype_2.5.1-1_all.deb ... 130s Unpacking python3-freetype (2.5.1-1) ... 130s Selecting previously unselected package python3-rlpycairo. 130s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 130s Unpacking python3-rlpycairo (0.3.0-3) ... 130s Selecting previously unselected package python3-reportlab. 130s Preparing to unpack .../54-python3-reportlab_4.3.1-1_all.deb ... 130s Unpacking python3-reportlab (4.3.1-1) ... 130s Selecting previously unselected package xml-core. 130s Preparing to unpack .../55-xml-core_0.19_all.deb ... 130s Unpacking xml-core (0.19) ... 130s Selecting previously unselected package w3c-sgml-lib. 130s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 130s Unpacking w3c-sgml-lib (1.3-3) ... 130s Selecting previously unselected package python3-biopython. 130s Preparing to unpack .../57-python3-biopython_1.85+dfsg-2build1_ppc64el.deb ... 130s Unpacking python3-biopython (1.85+dfsg-2build1) ... 130s Selecting previously unselected package python3-soupsieve. 130s Preparing to unpack .../58-python3-soupsieve_2.6-1_all.deb ... 130s Unpacking python3-soupsieve (2.6-1) ... 130s Selecting previously unselected package python3-bs4. 130s Preparing to unpack .../59-python3-bs4_4.13.3-1_all.deb ... 130s Unpacking python3-bs4 (4.13.3-1) ... 130s Selecting previously unselected package python3-dendropy. 130s Preparing to unpack .../60-python3-dendropy_4.6.1-2_all.deb ... 130s Unpacking python3-dendropy (4.6.1-2) ... 130s Selecting previously unselected package libjs-jquery. 130s Preparing to unpack .../61-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 130s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 130s Selecting previously unselected package libjs-jquery-ui. 130s Preparing to unpack .../62-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 130s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 130s Selecting previously unselected package fonts-lyx. 130s Preparing to unpack .../63-fonts-lyx_2.4.3-1_all.deb ... 130s Unpacking fonts-lyx (2.4.3-1) ... 130s Selecting previously unselected package python-matplotlib-data. 130s Preparing to unpack .../64-python-matplotlib-data_3.8.3-7build1_all.deb ... 130s Unpacking python-matplotlib-data (3.8.3-7build1) ... 130s Selecting previously unselected package python3-dateutil. 130s Preparing to unpack .../65-python3-dateutil_2.9.0-3_all.deb ... 130s Unpacking python3-dateutil (2.9.0-3) ... 130s Selecting previously unselected package python3-contourpy. 130s Preparing to unpack .../66-python3-contourpy_1.3.1-1build1_ppc64el.deb ... 130s Unpacking python3-contourpy (1.3.1-1build1) ... 130s Selecting previously unselected package python3-cycler. 130s Preparing to unpack .../67-python3-cycler_0.12.1-1_all.deb ... 130s Unpacking python3-cycler (0.12.1-1) ... 130s Selecting previously unselected package python3-brotli. 130s Preparing to unpack .../68-python3-brotli_1.1.0-2build4_ppc64el.deb ... 130s Unpacking python3-brotli (1.1.0-2build4) ... 130s Selecting previously unselected package python3-platformdirs. 130s Preparing to unpack .../69-python3-platformdirs_4.3.6-1_all.deb ... 130s Unpacking python3-platformdirs (4.3.6-1) ... 130s Selecting previously unselected package python3-fs. 130s Preparing to unpack .../70-python3-fs_2.4.16-7_all.deb ... 130s Unpacking python3-fs (2.4.16-7) ... 131s Selecting previously unselected package libxslt1.1:ppc64el. 131s Preparing to unpack .../71-libxslt1.1_1.1.39-0exp1ubuntu2_ppc64el.deb ... 131s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu2) ... 131s Selecting previously unselected package python3-lxml:ppc64el. 131s Preparing to unpack .../72-python3-lxml_5.3.1-1build1_ppc64el.deb ... 131s Unpacking python3-lxml:ppc64el (5.3.1-1build1) ... 131s Selecting previously unselected package python3-lz4. 131s Preparing to unpack .../73-python3-lz4_4.4.0+dfsg-1build1_ppc64el.deb ... 131s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 131s Selecting previously unselected package python3-decorator. 131s Preparing to unpack .../74-python3-decorator_5.1.1-5_all.deb ... 131s Unpacking python3-decorator (5.1.1-5) ... 131s Selecting previously unselected package liblbfgsb0:ppc64el. 131s Preparing to unpack .../75-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 131s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 131s Selecting previously unselected package python3-scipy. 131s Preparing to unpack .../76-python3-scipy_1.14.1-4ubuntu1_ppc64el.deb ... 131s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 131s Selecting previously unselected package python3-mpmath. 131s Preparing to unpack .../77-python3-mpmath_1.3.0-1_all.deb ... 131s Unpacking python3-mpmath (1.3.0-1) ... 131s Selecting previously unselected package python3-sympy. 131s Preparing to unpack .../78-python3-sympy_1.13.3-5_all.deb ... 131s Unpacking python3-sympy (1.13.3-5) ... 132s Selecting previously unselected package python3-ufolib2. 132s Preparing to unpack .../79-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 132s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 132s Selecting previously unselected package python3-unicodedata2. 132s Preparing to unpack .../80-python3-unicodedata2_15.1.0+ds-1build3_ppc64el.deb ... 132s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 132s Selecting previously unselected package unicode-data. 132s Preparing to unpack .../81-unicode-data_15.1.0-1_all.deb ... 132s Unpacking unicode-data (15.1.0-1) ... 132s Selecting previously unselected package python3-fonttools. 132s Preparing to unpack .../82-python3-fonttools_4.55.3-2build1_ppc64el.deb ... 132s Unpacking python3-fonttools (4.55.3-2build1) ... 132s Selecting previously unselected package python3-kiwisolver. 132s Preparing to unpack .../83-python3-kiwisolver_1.4.7-3build1_ppc64el.deb ... 132s Unpacking python3-kiwisolver (1.4.7-3build1) ... 132s Selecting previously unselected package python3-packaging. 132s Preparing to unpack .../84-python3-packaging_24.2-1_all.deb ... 132s Unpacking python3-packaging (24.2-1) ... 132s Selecting previously unselected package libqhull-r8.0:ppc64el. 132s Preparing to unpack .../85-libqhull-r8.0_2020.2-6build1_ppc64el.deb ... 132s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ... 132s Selecting previously unselected package python3-matplotlib. 132s Preparing to unpack .../86-python3-matplotlib_3.8.3-7build1_ppc64el.deb ... 132s Unpacking python3-matplotlib (3.8.3-7build1) ... 133s Selecting previously unselected package mummer. 133s Preparing to unpack .../87-mummer_3.23+dfsg-8_ppc64el.deb ... 133s Unpacking mummer (3.23+dfsg-8) ... 133s Selecting previously unselected package python3-pymummer. 133s Preparing to unpack .../88-python3-pymummer_0.11.0-5_all.deb ... 133s Unpacking python3-pymummer (0.11.0-5) ... 133s Selecting previously unselected package python3-pysam. 133s Preparing to unpack .../89-python3-pysam_0.23.0+ds-1build1_ppc64el.deb ... 133s Unpacking python3-pysam (0.23.0+ds-1build1) ... 133s Selecting previously unselected package libfml0:ppc64el. 133s Preparing to unpack .../90-libfml0_0.1+git20221215.85f159e-1_ppc64el.deb ... 133s Unpacking libfml0:ppc64el (0.1+git20221215.85f159e-1) ... 133s Selecting previously unselected package libminimap0:ppc64el. 133s Preparing to unpack .../91-libminimap0_0.2-8_ppc64el.deb ... 133s Unpacking libminimap0:ppc64el (0.2-8) ... 133s Selecting previously unselected package bowtie2. 133s Preparing to unpack .../92-bowtie2_2.5.4-1_ppc64el.deb ... 133s Unpacking bowtie2 (2.5.4-1) ... 133s Selecting previously unselected package cd-hit. 133s Preparing to unpack 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Selecting previously unselected package ariba. 133s Preparing to unpack .../99-ariba_2.14.7+ds-7_ppc64el.deb ... 133s Unpacking ariba (2.14.7+ds-7) ... 133s Setting up libhtscodecs2:ppc64el (1.6.1-2) ... 133s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 133s Setting up liblcms2-2:ppc64el (2.16-2) ... 133s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 133s Setting up libsharpyuv0:ppc64el (1.5.0-0.1) ... 133s Setting up liblerc4:ppc64el (4.0.0+ds-5ubuntu1) ... 133s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ... 133s Setting up libgslcblas0:ppc64el (2.8+dfsg-5) ... 133s Setting up libmurmurhash2:ppc64el (1.6-1) ... 133s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 133s Setting up libxcb-render0:ppc64el (1.17.0-2) ... 133s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 133s Setting up fonts-lyx (2.4.3-1) ... 133s Setting up x11-common (1:7.7+23ubuntu3) ... 134s Setting up libdeflate0:ppc64el (1.23-1) ... 134s Setting up libqhull-r8.0:ppc64el 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(11.1.0-5build1) ... 149s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 149s Setting up python3-cairo (1.26.1-2build2) ... 149s Setting up blt (2.5.3+dfsg-8) ... 149s Setting up python3-tk:ppc64el (3.13.2-1) ... 149s Setting up python3-pil.imagetk:ppc64el (11.1.0-5build1) ... 149s Setting up python3-rlpycairo (0.3.0-3) ... 149s Setting up python3-reportlab (4.3.1-1) ... 149s Setting up python3-fonttools (4.55.3-2build1) ... 150s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 150s Setting up python3-matplotlib (3.8.3-7build1) ... 152s Processing triggers for libc-bin (2.41-1ubuntu1) ... 152s Processing triggers for man-db (2.13.0-1) ... 153s Processing triggers for sgml-base (1.31) ... 153s Setting up w3c-sgml-lib (1.3-3) ... 183s Setting up python3-biopython (1.85+dfsg-2build1) ... 184s Setting up ariba (2.14.7+ds-7) ... 185s autopkgtest [01:20:55]: test test-example: [----------------------- 188s ARIBA version: 2.14.6 188s 188s External dependencies: 188s bowtie2 2.5.4 /usr/bin/bowtie2 188s cdhit 4.8.1 /usr/bin/cd-hit-est 188s nucmer 3.1 /usr/bin/nucmer 188s 188s External dependencies OK: True 188s 188s Python version: 188s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 188s 188s Python packages: 188s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 188s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 188s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 188s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 188s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 188s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 188s 188s Python packages OK: True 188s 188s Everything looks OK: True 188s 188s Loading and checking input data 188s 188s Running cdhit 188s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.lqpekeiNtb/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.lqpekeiNtb/foo/tmp.run_cd-hit.6306jtet/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 188s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.lqpekeiNtb/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.lqpekeiNtb/foo/tmp.run_cd-hit.l57ggb91/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 188s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.lqpekeiNtb/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.lqpekeiNtb/foo/tmp.run_cd-hit.0wtdp0_q/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 188s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.lqpekeiNtb/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.lqpekeiNtb/foo/tmp.run_cd-hit.hbcjaghe/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 188s 188s Writing clusters to file. 10 in total 189s Found reads file: reads_1.fq 189s Found reads file: reads_2.fq 189s ARIBA version: 2.14.6 189s 189s External dependencies: 189s bowtie2 2.5.4 /usr/bin/bowtie2 189s cdhit 4.8.1 /usr/bin/cd-hit-est 189s nucmer 3.1 /usr/bin/nucmer 189s 189s External dependencies OK: True 189s 189s Python version: 189s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 189s 189s Python packages: 189s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 189s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 189s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 189s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 189s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 189s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 189s 189s Python packages OK: True 189s 189s Everything looks OK: True 189s Temporary directory: /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk 189s ______________________ Mapping reads to clustered genes _______________________ 189s Finished mapping 189s 189s _____________________________ Generating clusters _____________________________ 189s syscall: sort -k1,1 -k 2,2n /tmp/tmp.lqpekeiNtb/foo/OUT/minimap.reads > /tmp/tmp.lqpekeiNtb/foo/OUT/read_store 189s Compressing file /tmp/tmp.lqpekeiNtb/foo/OUT/read_store 189s Found 51 proper read pairs from minimap 189s Total clusters to perform local assemblies: 9 189s 189s Insert size information from reads mapped to reference genes: 189s Insert size: 185.0 189s Insert sspace sd: 0.27 189s Max insert: 220.55 189s 189s ___________________________ Assembling each cluster ___________________________ 189s Will run 1 cluster(s) in parallel 189s Not constructing cluster cluster because it only has 2 reads (1 of 9) 189s Constructing cluster cluster_1 (2 of 9) 189s Constructing cluster cluster_2 (3 of 9) 189s Constructing cluster cluster_3 (4 of 9) 189s Constructing cluster cluster_4 (5 of 9) 189s Constructing cluster gene (6 of 9) 189s Constructing cluster gene_1 (7 of 9) 189s Constructing cluster noncoding (8 of 9) 189s Constructing cluster noncoding_1 (9 of 9) 189s Start running cluster cluster_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_1 191s cluster_1 detected 1 threads available to it 191s cluster_1 reported completion 191s Finished running cluster cluster_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_1 191s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_1 191s Start running cluster cluster_2 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_2 194s cluster_2 detected 1 threads available to it 194s cluster_2 reported completion 194s Finished running cluster cluster_2 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_2 194s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_2 194s Start running cluster cluster_3 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_3 196s cluster_3 detected 1 threads available to it 196s cluster_3 reported completion 196s Finished running cluster cluster_3 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_3 196s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_3 196s Start running cluster cluster_4 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_4 198s cluster_4 detected 1 threads available to it 198s cluster_4 reported completion 198s Finished running cluster cluster_4 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_4 198s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/cluster_4 198s Start running cluster gene in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene 201s gene detected 1 threads available to it 201s gene reported completion 201s Finished running cluster gene in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene 201s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene 201s Start running cluster gene_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene_1 203s gene_1 detected 1 threads available to it 203s gene_1 reported completion 203s Finished running cluster gene_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene_1 203s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/gene_1 203s Start running cluster noncoding in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding 205s noncoding detected 1 threads available to it 205s noncoding reported completion 205s Finished running cluster noncoding in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding 205s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding 205s Start running cluster noncoding_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding_1 207s noncoding_1 detected 1 threads available to it 207s noncoding_1 reported completion 207s Finished running cluster noncoding_1 in directory /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding_1 207s Deleting cluster dir /tmp/tmp.lqpekeiNtb/foo/OUT/ariba.tmp.ksyc8xnk/noncoding_1 207s Final value of remaining_clusters counter: Value('l', 0) 207s Finished assembling clusters 207s 207s _______________________________ Writing reports _______________________________ 207s Making /tmp/tmp.lqpekeiNtb/foo/OUT/debug.report.tsv 207s Making /tmp/tmp.lqpekeiNtb/foo/OUT/report.tsv 207s 207s ____________________ Writing fasta of assembled sequences _____________________ 207s /tmp/tmp.lqpekeiNtb/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.lqpekeiNtb/foo/OUT/assembled_genes.fa.gz 207s 207s __________________________ Catting cluster log files __________________________ 207s Writing file /tmp/tmp.lqpekeiNtb/foo/OUT/log.clusters.gz 207s 207s _______________________________ Cleaning files ________________________________ 207s Deleting Logs directory /tmp/tmp.lqpekeiNtb/foo/OUT/Logs 207s Deleting reads store files /tmp/tmp.lqpekeiNtb/foo/OUT/read_store.gz[.tbi] 207s 207s All done! 207s 208s Running ARIBA on test data... 208s ------------------------------------------------------------------------------- 208s |=============================================================================| 208s | Preparing input data | 208s |=============================================================================| 208s ------------------------------------------------------------------------------- 208s Made output directory ./foo. Copying test data files into it: 208s copied ref_seqs.fa 208s copied metadata.tsv 208s copied reads_1.fq 208s copied reads_2.fq 208s ------------------------------------------------------------------------------- 208s |=============================================================================| 208s | Try running ariba prepareref | 208s |=============================================================================| 208s ------------------------------------------------------------------------------- 208s 208s Running ariba prepareref with: 208s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 208s 208s 208s ariba prepareref finished OK 208s ------------------------------------------------------------------------------- 208s |=============================================================================| 208s | Try running ariba run | 208s |=============================================================================| 208s ------------------------------------------------------------------------------- 208s 208s Running ARIBA with: 208s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 208s 208s 208s ariba run finished OK 208s Finished run on test data OK 208s autopkgtest [01:21:18]: test test-example: -----------------------] 208s test-example PASS 208s autopkgtest [01:21:18]: test test-example: - - - - - - - - - - results - - - - - - - - - - 209s autopkgtest [01:21:19]: @@@@@@@@@@@@@@@@@@@@ summary 209s test-example PASS 213s nova [W] Using flock in prodstack6-ppc64el 213s Creating nova instance adt-plucky-ppc64el-ariba-20250308-011750-juju-7f2275-prod-proposed-migration-environment-2-3116446e-28d2-4bfd-8c82-a1e0dd25be9f from image adt/ubuntu-plucky-ppc64el-server-20250307.img (UUID 10039a41-be3c-4520-8be3-e4577afe5e2b)... 213s nova [W] Timed out waiting for cfb8a0fd-7eb9-4a29-bc54-501a3ded88f5 to get deleted.