0s autopkgtest [19:20:57]: starting date and time: 2025-03-06 19:20:57+0000 0s autopkgtest [19:20:57]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:20:57]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.njleyd61/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-35.secgroup --name adt-plucky-arm64-ariba-20250306-192056-juju-7f2275-prod-proposed-migration-environment-2-fad496ee-b96c-40b2-8d27-240930a6ed95 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 149s autopkgtest [19:23:26]: testbed dpkg architecture: arm64 150s autopkgtest [19:23:27]: testbed apt version: 2.9.31ubuntu1 150s autopkgtest [19:23:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 150s autopkgtest [19:23:27]: testbed release detected to be: None 151s autopkgtest [19:23:28]: updating testbed package index (apt update) 152s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 152s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 152s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 152s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 152s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [562 kB] 152s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [12.2 kB] 152s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [59.9 kB] 152s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [5496 B] 152s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [94.2 kB] 152s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.9 kB] 152s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [364 kB] 153s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4204 B] 153s Fetched 1263 kB in 1s (1381 kB/s) 154s Reading package lists... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s Calculating upgrade... 156s Calculating upgrade... 156s The following packages will be upgraded: 156s libaudit-common libaudit1 libbrotli1 libcap-ng0 python3-dbus python3-gi 157s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 758 kB of archives. 157s After this operation, 712 kB disk space will be freed. 157s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-4build1 [15.0 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit1 arm64 1:4.0.2-2ubuntu2 [54.3 kB] 157s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dbus arm64 1.3.2-5build5 [99.8 kB] 157s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-gi arm64 3.50.0-4build1 [242 kB] 157s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libbrotli1 arm64 1.1.0-2build4 [340 kB] 158s Fetched 758 kB in 1s (1290 kB/s) 158s (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 ... 116820 files and directories currently installed.) 158s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ... 158s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 158s Setting up libaudit-common (1:4.0.2-2ubuntu2) ... 158s (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 ... 116820 files and directories currently installed.) 158s Preparing to unpack .../libcap-ng0_0.8.5-4build1_arm64.deb ... 158s Unpacking libcap-ng0:arm64 (0.8.5-4build1) over (0.8.5-4) ... 158s Setting up libcap-ng0:arm64 (0.8.5-4build1) ... 158s (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 ... 116820 files and directories currently installed.) 158s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_arm64.deb ... 158s Unpacking libaudit1:arm64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 158s Setting up libaudit1:arm64 (1:4.0.2-2ubuntu2) ... 158s (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 ... 116820 files and directories currently installed.) 158s Preparing to unpack .../python3-dbus_1.3.2-5build5_arm64.deb ... 159s Unpacking python3-dbus (1.3.2-5build5) over (1.3.2-5build4) ... 159s Preparing to unpack .../python3-gi_3.50.0-4build1_arm64.deb ... 159s Unpacking python3-gi (3.50.0-4build1) over (3.50.0-4) ... 159s Preparing to unpack .../libbrotli1_1.1.0-2build4_arm64.deb ... 159s Unpacking libbrotli1:arm64 (1.1.0-2build4) over (1.1.0-2build3) ... 159s Setting up python3-dbus (1.3.2-5build5) ... 159s Setting up libbrotli1:arm64 (1.1.0-2build4) ... 159s Setting up python3-gi (3.50.0-4build1) ... 159s Processing triggers for man-db (2.13.0-1) ... 160s Processing triggers for libc-bin (2.41-1ubuntu1) ... 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 161s Solving dependencies... 161s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 161s autopkgtest [19:23:38]: upgrading testbed (apt dist-upgrade and autopurge) 161s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 163s Entering ResolveByKeep 163s 164s Calculating upgrade... 164s The following package was automatically installed and is no longer required: 164s python3.12-gdbm 164s Use 'sudo apt autoremove' to remove it. 164s The following packages will be upgraded: 164s python3-gdbm 164s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 8708 B of archives. 164s After this operation, 0 B of additional disk space will be used. 164s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.13.2-1 [8708 B] 165s Fetched 8708 B in 0s (55.4 kB/s) 165s (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 ... 116817 files and directories currently installed.) 165s Preparing to unpack .../python3-gdbm_3.13.2-1_arm64.deb ... 165s Unpacking python3-gdbm:arm64 (3.13.2-1) over (3.13.1-1) ... 165s Setting up python3-gdbm:arm64 (3.13.2-1) ... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 166s Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s Solving dependencies... 167s The following packages will be REMOVED: 167s python3.12-gdbm* 167s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 167s After this operation, 140 kB disk space will be freed. 167s (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 ... 116817 files and directories currently installed.) 167s Removing python3.12-gdbm (3.12.9-1) ... 171s autopkgtest [19:23:48]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 14 14:51:45 UTC 2025 172s autopkgtest [19:23:49]: @@@@@@@@@@@@@@@@@@@@ apt-source ariba 174s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (dsc) [2435 B] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (tar) [1920 kB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ariba 2.14.7+ds-7 (diff) [11.5 kB] 174s gpgv: Signature made Thu Jan 30 21:44:32 2025 UTC 174s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 174s gpgv: issuer "emollier@debian.org" 174s gpgv: Can't check signature: No public key 174s dpkg-source: warning: cannot verify inline signature for ./ariba_2.14.7+ds-7.dsc: no acceptable signature found 175s autopkgtest [19:23:52]: testing package ariba version 2.14.7+ds-7 175s autopkgtest [19:23:52]: build not needed 180s autopkgtest [19:23:57]: test test-example: preparing testbed 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 182s Starting pkgProblemResolver with broken count: 0 182s Starting 2 pkgProblemResolver with broken count: 0 182s Done 184s The following NEW packages will be installed: 184s ariba blt bowtie2 cd-hit fastaq fontconfig-config fonts-dejavu-core 184s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 184s libcapnp-1.1.0 libdeflate0 libfml0 libfontconfig1 libfontenc1 libgfortran5 184s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhts3t64 184s libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 184s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libminimap0 184s libmurmurhash2 libopenjp2-7 libpixman-1-0 libqhull-r8.0 libraqm0 184s libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 184s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 mash 184s mummer python-matplotlib-data python3-biopython python3-brotli python3-bs4 184s python3-cairo python3-contourpy python3-cycler python3-dateutil 184s python3-decorator python3-dendropy python3-fonttools python3-freetype 184s python3-fs python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 184s python3-mpmath python3-numpy python3-numpy-dev python3-packaging python3-pil 184s python3-pil.imagetk python3-platformdirs python3-pymummer python3-pysam 184s python3-reportlab python3-rlpycairo python3-scipy python3-soupsieve 184s python3-sympy python3-tk python3-ufolib2 python3-unicodedata2 python3.13-tk 184s samtools sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 184s xfonts-encodings xfonts-utils xml-core 184s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 184s Need to get 101 MB of archives. 184s After this operation, 446 MB of additional disk space will be used. 184s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-2 [145 kB] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 185s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 185s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-2 [4583 kB] 186s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 186s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 186s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 186s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 186s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 samtools arm64 1.21-1 [609 kB] 186s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 fastaq all 3.17.0-9 [48.2 kB] 186s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 186s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 186s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 186s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 186s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 186s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 186s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 186s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 187s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 187s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 187s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 187s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 187s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 187s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 187s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-1 [106 kB] 187s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 187s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 187s Get:29 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.13.2-1 [9818 B] 187s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5 [9948 B] 187s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 187s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 187s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 187s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 187s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 187s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 187s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 187s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 187s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 187s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 187s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 187s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 187s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 187s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 187s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 187s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 187s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 187s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 187s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 187s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 187s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 187s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build2 [122 kB] 187s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 187s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 187s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 187s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 187s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 187s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 187s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-soupsieve all 2.6-1 [33.0 kB] 187s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-bs4 all 4.13.3-1 [136 kB] 187s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dendropy all 4.6.1-2 [278 kB] 187s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 187s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 187s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 187s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 187s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 187s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 187s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 187s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 187s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 187s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 187s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 187s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 187s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 187s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 187s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 187s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu1 [19.5 MB] 188s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 188s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 188s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 188s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build3 [360 kB] 188s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 188s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 188s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 188s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 188s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 188s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 189s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 189s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymummer all 0.11.0-5 [17.3 kB] 189s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 189s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfml0 arm64 0.1+git20221215.85f159e-1 [74.4 kB] 189s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libminimap0 arm64 0.2-8 [22.6 kB] 189s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 bowtie2 arm64 2.5.4-1 [1380 kB] 189s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 cd-hit arm64 4.8.1-4 [522 kB] 189s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcapnp-1.1.0 arm64 1.1.0-2 [1371 kB] 189s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 189s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 189s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmurmurhash2 arm64 1.6-1 [6098 B] 189s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 mash arm64 2.3+dfsg-6build2 [149 kB] 189s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 ariba arm64 2.14.7+ds-7 [2029 kB] 190s Fetched 101 MB in 5s (20.1 MB/s) 190s Selecting previously unselected package python3-numpy-dev:arm64. 190s (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 ... 116812 files and directories currently installed.) 190s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-2_arm64.deb ... 190s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-2) ... 190s Selecting previously unselected package libblas3:arm64. 190s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 190s Unpacking libblas3:arm64 (3.12.1-2) ... 190s Selecting previously unselected package libgfortran5:arm64. 190s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 190s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 190s Selecting previously unselected package liblapack3:arm64. 190s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 190s Unpacking liblapack3:arm64 (3.12.1-2) ... 190s Selecting previously unselected package python3-numpy. 190s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-2_arm64.deb ... 190s Unpacking python3-numpy (1:2.2.3+ds-2) ... 190s Selecting previously unselected package sgml-base. 190s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 190s Unpacking sgml-base (1.31) ... 190s Selecting previously unselected package libdeflate0:arm64. 190s Preparing to unpack .../06-libdeflate0_1.23-1_arm64.deb ... 190s Unpacking libdeflate0:arm64 (1.23-1) ... 190s Selecting previously unselected package libhtscodecs2:arm64. 190s Preparing to unpack .../07-libhtscodecs2_1.6.1-2_arm64.deb ... 190s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 190s Selecting previously unselected package libhts3t64:arm64. 190s Preparing to unpack .../08-libhts3t64_1.21+ds-1_arm64.deb ... 190s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 191s Selecting previously unselected package samtools. 191s Preparing to unpack .../09-samtools_1.21-1_arm64.deb ... 191s Unpacking samtools (1.21-1) ... 191s Selecting previously unselected package fastaq. 191s Preparing to unpack .../10-fastaq_3.17.0-9_all.deb ... 191s Unpacking fastaq (3.17.0-9) ... 191s Selecting previously unselected package libtcl8.6:arm64. 191s Preparing to unpack .../11-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 191s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 191s Selecting previously unselected package fonts-dejavu-mono. 191s Preparing to unpack .../12-fonts-dejavu-mono_2.37-8_all.deb ... 191s Unpacking fonts-dejavu-mono (2.37-8) ... 191s Selecting previously unselected package fonts-dejavu-core. 191s Preparing to unpack .../13-fonts-dejavu-core_2.37-8_all.deb ... 191s Unpacking fonts-dejavu-core (2.37-8) ... 191s Selecting previously unselected package libfontenc1:arm64. 191s Preparing to unpack .../14-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 191s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 191s Selecting previously unselected package x11-common. 191s Preparing to unpack .../15-x11-common_1%3a7.7+23ubuntu3_all.deb ... 191s Unpacking x11-common (1:7.7+23ubuntu3) ... 191s Selecting previously unselected package xfonts-encodings. 191s Preparing to unpack .../16-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 191s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 191s Selecting previously unselected package xfonts-utils. 191s Preparing to unpack .../17-xfonts-utils_1%3a7.7+7_arm64.deb ... 191s Unpacking xfonts-utils (1:7.7+7) ... 191s Selecting previously unselected package fonts-urw-base35. 191s Preparing to unpack .../18-fonts-urw-base35_20200910-8_all.deb ... 191s Unpacking fonts-urw-base35 (20200910-8) ... 191s Selecting previously unselected package fontconfig-config. 191s Preparing to unpack .../19-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 192s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 192s Selecting previously unselected package libfontconfig1:arm64. 192s Preparing to unpack .../20-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 192s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 192s Selecting previously unselected package libxrender1:arm64. 192s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 192s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 192s Selecting previously unselected package libxft2:arm64. 192s Preparing to unpack .../22-libxft2_2.3.6-1build1_arm64.deb ... 192s Unpacking libxft2:arm64 (2.3.6-1build1) ... 192s Selecting previously unselected package libxss1:arm64. 192s Preparing to unpack .../23-libxss1_1%3a1.2.3-1build3_arm64.deb ... 192s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 192s Selecting previously unselected package libtk8.6:arm64. 192s Preparing to unpack .../24-libtk8.6_8.6.16-1_arm64.deb ... 192s Unpacking libtk8.6:arm64 (8.6.16-1) ... 192s Selecting previously unselected package python3.13-tk. 192s Preparing to unpack .../25-python3.13-tk_3.13.2-1_arm64.deb ... 192s Unpacking python3.13-tk (3.13.2-1) ... 192s Selecting previously unselected package tk8.6-blt2.5. 192s Preparing to unpack .../26-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 192s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 192s Selecting previously unselected package blt. 192s Preparing to unpack .../27-blt_2.5.3+dfsg-8_arm64.deb ... 192s Unpacking blt (2.5.3+dfsg-8) ... 192s Selecting previously unselected package python3-tk:arm64. 192s Preparing to unpack .../28-python3-tk_3.13.2-1_arm64.deb ... 192s Unpacking python3-tk:arm64 (3.13.2-1) ... 193s Selecting previously unselected package python3-pil.imagetk:arm64. 193s Preparing to unpack .../29-python3-pil.imagetk_11.1.0-5_arm64.deb ... 193s Unpacking python3-pil.imagetk:arm64 (11.1.0-5) ... 193s Selecting previously unselected package libgomp1:arm64. 193s Preparing to unpack .../30-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 193s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 193s Selecting previously unselected package libimagequant0:arm64. 193s Preparing to unpack .../31-libimagequant0_2.18.0-1build1_arm64.deb ... 193s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 193s Selecting previously unselected package libjpeg-turbo8:arm64. 193s Preparing to unpack .../32-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 193s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 193s Selecting previously unselected package libjpeg8:arm64. 193s Preparing to unpack .../33-libjpeg8_8c-2ubuntu11_arm64.deb ... 193s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 193s Selecting previously unselected package liblcms2-2:arm64. 193s Preparing to unpack .../34-liblcms2-2_2.16-2_arm64.deb ... 193s Unpacking liblcms2-2:arm64 (2.16-2) ... 193s Selecting previously unselected package libopenjp2-7:arm64. 193s Preparing to unpack .../35-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 193s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 193s Selecting previously unselected package libgraphite2-3:arm64. 193s Preparing to unpack .../36-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 193s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 193s Selecting previously unselected package libharfbuzz0b:arm64. 193s Preparing to unpack .../37-libharfbuzz0b_10.2.0-1_arm64.deb ... 193s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 193s Selecting previously unselected package libraqm0:arm64. 193s Preparing to unpack .../38-libraqm0_0.10.2-1_arm64.deb ... 193s Unpacking libraqm0:arm64 (0.10.2-1) ... 193s Selecting previously unselected package libjbig0:arm64. 193s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 193s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 193s Selecting previously unselected package liblerc4:arm64. 193s Preparing to unpack .../40-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 193s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 193s Selecting previously unselected package libsharpyuv0:arm64. 193s Preparing to unpack .../41-libsharpyuv0_1.5.0-0.1_arm64.deb ... 193s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 193s Selecting previously unselected package libwebp7:arm64. 194s Preparing to unpack .../42-libwebp7_1.5.0-0.1_arm64.deb ... 194s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 194s Selecting previously unselected package libtiff6:arm64. 194s Preparing to unpack .../43-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 194s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 194s Selecting previously unselected package libwebpdemux2:arm64. 194s Preparing to unpack .../44-libwebpdemux2_1.5.0-0.1_arm64.deb ... 194s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 194s Selecting previously unselected package libwebpmux3:arm64. 194s Preparing to unpack .../45-libwebpmux3_1.5.0-0.1_arm64.deb ... 194s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 194s Selecting previously unselected package python3-pil:arm64. 194s Preparing to unpack .../46-python3-pil_11.1.0-5_arm64.deb ... 194s Unpacking python3-pil:arm64 (11.1.0-5) ... 194s Selecting previously unselected package libpixman-1-0:arm64. 194s Preparing to unpack .../47-libpixman-1-0_0.44.0-3_arm64.deb ... 194s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 194s Selecting previously unselected package libxcb-render0:arm64. 194s Preparing to unpack .../48-libxcb-render0_1.17.0-2_arm64.deb ... 194s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 194s Selecting previously unselected package libxcb-shm0:arm64. 194s Preparing to unpack .../49-libxcb-shm0_1.17.0-2_arm64.deb ... 194s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 194s Selecting previously unselected package libcairo2:arm64. 194s Preparing to unpack .../50-libcairo2_1.18.2-2_arm64.deb ... 194s Unpacking libcairo2:arm64 (1.18.2-2) ... 194s Selecting previously unselected package python3-cairo. 194s Preparing to unpack .../51-python3-cairo_1.26.1-2build2_arm64.deb ... 194s Unpacking python3-cairo (1.26.1-2build2) ... 194s Selecting previously unselected package python3-freetype. 194s Preparing to unpack .../52-python3-freetype_2.5.1-1_all.deb ... 194s Unpacking python3-freetype (2.5.1-1) ... 194s Selecting previously unselected package python3-rlpycairo. 194s Preparing to unpack .../53-python3-rlpycairo_0.3.0-3_all.deb ... 194s Unpacking python3-rlpycairo (0.3.0-3) ... 194s Selecting previously unselected package python3-reportlab. 194s Preparing to unpack .../54-python3-reportlab_4.3.1-1_all.deb ... 194s Unpacking python3-reportlab (4.3.1-1) ... 194s Selecting previously unselected package xml-core. 194s Preparing to unpack .../55-xml-core_0.19_all.deb ... 194s Unpacking xml-core (0.19) ... 194s Selecting previously unselected package w3c-sgml-lib. 194s Preparing to unpack .../56-w3c-sgml-lib_1.3-3_all.deb ... 194s Unpacking w3c-sgml-lib (1.3-3) ... 194s Selecting previously unselected package python3-biopython. 194s Preparing to unpack .../57-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 194s Unpacking python3-biopython (1.85+dfsg-2build1) ... 195s Selecting previously unselected package python3-soupsieve. 195s Preparing to unpack .../58-python3-soupsieve_2.6-1_all.deb ... 195s Unpacking python3-soupsieve (2.6-1) ... 195s Selecting previously unselected package python3-bs4. 195s Preparing to unpack .../59-python3-bs4_4.13.3-1_all.deb ... 195s Unpacking python3-bs4 (4.13.3-1) ... 195s Selecting previously unselected package python3-dendropy. 195s Preparing to unpack .../60-python3-dendropy_4.6.1-2_all.deb ... 195s Unpacking python3-dendropy (4.6.1-2) ... 195s Selecting previously unselected package libjs-jquery. 195s Preparing to unpack .../61-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 195s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 195s Selecting previously unselected package libjs-jquery-ui. 195s Preparing to unpack .../62-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 195s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 195s Selecting previously unselected package fonts-lyx. 195s Preparing to unpack .../63-fonts-lyx_2.4.3-1_all.deb ... 195s Unpacking fonts-lyx (2.4.3-1) ... 195s Selecting previously unselected package python-matplotlib-data. 195s Preparing to unpack .../64-python-matplotlib-data_3.8.3-7build1_all.deb ... 195s Unpacking python-matplotlib-data (3.8.3-7build1) ... 195s Selecting previously unselected package python3-dateutil. 195s Preparing to unpack .../65-python3-dateutil_2.9.0-3_all.deb ... 195s Unpacking python3-dateutil (2.9.0-3) ... 195s Selecting previously unselected package python3-contourpy. 195s Preparing to unpack .../66-python3-contourpy_1.3.1-1build1_arm64.deb ... 195s Unpacking python3-contourpy (1.3.1-1build1) ... 195s Selecting previously unselected package python3-cycler. 195s Preparing to unpack .../67-python3-cycler_0.12.1-1_all.deb ... 195s Unpacking python3-cycler (0.12.1-1) ... 195s Selecting previously unselected package python3-brotli. 195s Preparing to unpack .../68-python3-brotli_1.1.0-2build4_arm64.deb ... 195s Unpacking python3-brotli (1.1.0-2build4) ... 195s Selecting previously unselected package python3-platformdirs. 195s Preparing to unpack .../69-python3-platformdirs_4.3.6-1_all.deb ... 195s Unpacking python3-platformdirs (4.3.6-1) ... 195s Selecting previously unselected package python3-fs. 195s Preparing to unpack .../70-python3-fs_2.4.16-7_all.deb ... 195s Unpacking python3-fs (2.4.16-7) ... 195s Selecting previously unselected package libxslt1.1:arm64. 195s Preparing to unpack .../71-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 195s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 195s Selecting previously unselected package python3-lxml:arm64. 195s Preparing to unpack .../72-python3-lxml_5.3.1-1build1_arm64.deb ... 195s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 195s Selecting previously unselected package python3-lz4. 195s Preparing to unpack .../73-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 195s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 196s Selecting previously unselected package python3-decorator. 196s Preparing to unpack .../74-python3-decorator_5.1.1-5_all.deb ... 196s Unpacking python3-decorator (5.1.1-5) ... 196s Selecting previously unselected package liblbfgsb0:arm64. 196s Preparing to unpack .../75-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 196s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 196s Selecting previously unselected package python3-scipy. 196s Preparing to unpack .../76-python3-scipy_1.14.1-4ubuntu1_arm64.deb ... 196s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 196s Selecting previously unselected package python3-mpmath. 196s Preparing to unpack .../77-python3-mpmath_1.3.0-1_all.deb ... 196s Unpacking python3-mpmath (1.3.0-1) ... 197s Selecting previously unselected package python3-sympy. 197s Preparing to unpack .../78-python3-sympy_1.13.3-5_all.deb ... 197s Unpacking python3-sympy (1.13.3-5) ... 197s Selecting previously unselected package python3-ufolib2. 197s Preparing to unpack .../79-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 197s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 197s Selecting previously unselected package python3-unicodedata2. 197s Preparing to unpack .../80-python3-unicodedata2_15.1.0+ds-1build3_arm64.deb ... 197s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 197s Selecting previously unselected package unicode-data. 197s Preparing to unpack .../81-unicode-data_15.1.0-1_all.deb ... 197s Unpacking unicode-data (15.1.0-1) ... 197s Selecting previously unselected package python3-fonttools. 197s Preparing to unpack .../82-python3-fonttools_4.55.3-2build1_arm64.deb ... 197s Unpacking python3-fonttools (4.55.3-2build1) ... 198s Selecting previously unselected package python3-kiwisolver. 198s Preparing to unpack .../83-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 198s Unpacking python3-kiwisolver (1.4.7-3build1) ... 198s Selecting previously unselected package python3-packaging. 198s Preparing to unpack .../84-python3-packaging_24.2-1_all.deb ... 198s Unpacking python3-packaging (24.2-1) ... 198s Selecting previously unselected package libqhull-r8.0:arm64. 198s Preparing to unpack .../85-libqhull-r8.0_2020.2-6build1_arm64.deb ... 198s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 198s Selecting previously unselected package python3-matplotlib. 198s Preparing to unpack .../86-python3-matplotlib_3.8.3-7build1_arm64.deb ... 198s Unpacking python3-matplotlib (3.8.3-7build1) ... 198s Selecting previously unselected package mummer. 198s Preparing to unpack .../87-mummer_3.23+dfsg-8_arm64.deb ... 198s Unpacking mummer (3.23+dfsg-8) ... 198s Selecting previously unselected package python3-pymummer. 198s Preparing to unpack .../88-python3-pymummer_0.11.0-5_all.deb ... 198s Unpacking python3-pymummer (0.11.0-5) ... 198s Selecting previously unselected package python3-pysam. 198s Preparing to unpack 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unselected package libgslcblas0:arm64. 199s Preparing to unpack .../95-libgslcblas0_2.8+dfsg-5_arm64.deb ... 199s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... 199s Selecting previously unselected package libgsl28:arm64. 199s Preparing to unpack .../96-libgsl28_2.8+dfsg-5_arm64.deb ... 199s Unpacking libgsl28:arm64 (2.8+dfsg-5) ... 199s Selecting previously unselected package libmurmurhash2:arm64. 199s Preparing to unpack .../97-libmurmurhash2_1.6-1_arm64.deb ... 199s Unpacking libmurmurhash2:arm64 (1.6-1) ... 199s Selecting previously unselected package mash. 200s Preparing to unpack .../98-mash_2.3+dfsg-6build2_arm64.deb ... 200s Unpacking mash (2.3+dfsg-6build2) ... 200s Selecting previously unselected package ariba. 200s Preparing to unpack .../99-ariba_2.14.7+ds-7_arm64.deb ... 200s Unpacking ariba (2.14.7+ds-7) ... 200s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 200s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 200s Setting up liblcms2-2:arm64 (2.16-2) ... 200s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 200s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 200s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 200s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 200s Setting up libgslcblas0:arm64 (2.8+dfsg-5) ... 200s Setting up libmurmurhash2:arm64 (1.6-1) ... 200s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 200s Setting up libxcb-render0:arm64 (1.17.0-2) ... 200s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 200s Setting up fonts-lyx (2.4.3-1) ... 200s Setting up x11-common (1:7.7+23ubuntu3) ... 200s Setting up libdeflate0:arm64 (1.23-1) ... 200s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 200s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 200s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 200s Setting up python3-freetype (2.5.1-1) ... 201s Setting up libfml0:arm64 (0.1+git20221215.85f159e-1) ... 201s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 201s Setting up python3-platformdirs (4.3.6-1) ... 201s Setting up bowtie2 (2.5.4-1) ... 201s Setting up python3-fs (2.4.16-7) ... 201s Setting up unicode-data (15.1.0-1) ... 201s Setting up python3-decorator (5.1.1-5) ... 201s Setting up libminimap0:arm64 (0.2-8) ... 201s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 201s Setting up libblas3:arm64 (3.12.1-2) ... 201s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 201s Setting up python3-packaging (24.2-1) ... 201s Setting up python3-brotli (1.1.0-2build4) ... 201s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 201s Setting up python3-cycler (0.12.1-1) ... 202s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 202s Setting up fonts-dejavu-mono (2.37-8) ... 202s Setting up python3-kiwisolver (1.4.7-3build1) ... 202s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-2) ... 202s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 202s Setting up fonts-dejavu-core (2.37-8) ... 202s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 202s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 202s Setting up libwebp7:arm64 (1.5.0-0.1) ... 202s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 202s Setting up mummer (3.23+dfsg-8) ... 202s Setting up libhts3t64:arm64 (1.21+ds-1) ... 202s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 202s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 202s Setting up python3-dateutil (2.9.0-3) ... 202s Setting up sgml-base (1.31) ... 202s Setting up libcapnp-1.1.0:arm64 (1.1.0-2) ... 202s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 202s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 202s Setting up python3-mpmath (1.3.0-1) ... 203s Setting up libgsl28:arm64 (2.8+dfsg-5) ... 203s Setting up python-matplotlib-data (3.8.3-7build1) ... 203s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 203s Setting up python3-dendropy (4.6.1-2) ... 203s Setting up python3-soupsieve (2.6-1) ... 204s Setting up cd-hit (4.8.1-4) ... 204s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 204s Setting up python3-sympy (1.13.3-5) ... 211s Setting up liblapack3:arm64 (3.12.1-2) ... 211s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 211s Setting up python3-pysam (0.23.0+ds-1build1) ... 211s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 211s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 211s Setting up xfonts-utils (1:7.7+7) ... 211s Setting up python3-bs4 (4.13.3-1) ... 211s Setting up samtools (1.21-1) ... 211s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 211s Setting up libraqm0:arm64 (0.10.2-1) ... 211s Setting up mash (2.3+dfsg-6build2) ... 211s Setting up python3-numpy (1:2.2.3+ds-2) ... 213s Setting up python3-lxml:arm64 (5.3.1-1build1) ... 213s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 213s Setting up xml-core (0.19) ... 214s Setting up python3-contourpy (1.3.1-1build1) ... 214s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 214s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 214s Setting up libxft2:arm64 (2.3.6-1build1) ... 214s Setting up python3-scipy (1.14.1-4ubuntu1) ... 217s Setting up libtk8.6:arm64 (8.6.16-1) ... 217s Setting up fastaq (3.17.0-9) ... 217s Setting up fonts-urw-base35 (20200910-8) ... 217s Setting up libcairo2:arm64 (1.18.2-2) ... 217s Setting up python3.13-tk (3.13.2-1) ... 218s Setting up python3-pymummer (0.11.0-5) ... 218s Setting up python3-pil:arm64 (11.1.0-5) ... 218s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 218s Setting up python3-cairo (1.26.1-2build2) ... 218s Setting up blt (2.5.3+dfsg-8) ... 218s Setting up python3-tk:arm64 (3.13.2-1) ... 218s Setting up python3-pil.imagetk:arm64 (11.1.0-5) ... 218s Setting up python3-rlpycairo (0.3.0-3) ... 218s Setting up python3-reportlab (4.3.1-1) ... 219s Setting up python3-fonttools (4.55.3-2build1) ... 220s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 220s Setting up python3-matplotlib (3.8.3-7build1) ... 222s Processing triggers for libc-bin (2.41-1ubuntu1) ... 222s Processing triggers for man-db (2.13.0-1) ... 223s Processing triggers for sgml-base (1.31) ... 223s Setting up w3c-sgml-lib (1.3-3) ... 252s Setting up python3-biopython (1.85+dfsg-2build1) ... 253s Setting up ariba (2.14.7+ds-7) ... 255s autopkgtest [19:25:12]: test test-example: [----------------------- 257s ARIBA version: 2.14.6 257s 257s External dependencies: 257s bowtie2 2.5.4 /usr/bin/bowtie2 257s cdhit 4.8.1 /usr/bin/cd-hit-est 257s nucmer 3.1 /usr/bin/nucmer 257s 257s External dependencies OK: True 257s 257s Python version: 257s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 257s 257s Python packages: 257s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 257s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 257s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 257s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 257s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 257s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 257s 257s Python packages OK: True 257s 257s Everything looks OK: True 257s 257s Loading and checking input data 257s 257s Running cdhit 258s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.5Pqo1iqXhC/foo/PREPAREREF/02.cdhit.noncoding.fa -o /tmp/tmp.5Pqo1iqXhC/foo/tmp.run_cd-hit._9v_9kt_/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 258s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.5Pqo1iqXhC/foo/PREPAREREF/02.cdhit.noncoding.varonly.fa -o /tmp/tmp.5Pqo1iqXhC/foo/tmp.run_cd-hit.hdhmiyjw/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 258s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.5Pqo1iqXhC/foo/PREPAREREF/02.cdhit.gene.fa -o /tmp/tmp.5Pqo1iqXhC/foo/tmp.run_cd-hit.ywocynuy/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 258s syscall: /usr/bin/cd-hit-est -i /tmp/tmp.5Pqo1iqXhC/foo/PREPAREREF/02.cdhit.gene.varonly.fa -o /tmp/tmp.5Pqo1iqXhC/foo/tmp.run_cd-hit.uovfu1w_/cdhit -c 0.9 -T 1 -s 0.0 -d 0 -bak 1 258s 258s Writing clusters to file. 10 in total 259s Found reads file: reads_1.fq 259s Found reads file: reads_2.fq 259s ARIBA version: 2.14.6 259s 259s External dependencies: 259s bowtie2 2.5.4 /usr/bin/bowtie2 259s cdhit 4.8.1 /usr/bin/cd-hit-est 259s nucmer 3.1 /usr/bin/nucmer 259s 259s External dependencies OK: True 259s 259s Python version: 259s 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 259s 259s Python packages: 259s ariba 2.14.6 /usr/lib/python3/dist-packages/ariba/__init__.py 259s bs4 4.13.3 /usr/lib/python3/dist-packages/bs4/__init__.py 259s dendropy 4.6.1 /usr/lib/python3/dist-packages/dendropy/__init__.py 259s pyfastaq 3.17.0 /usr/lib/python3/dist-packages/pyfastaq/__init__.py 259s pymummer 0.11.0 /usr/lib/python3/dist-packages/pymummer/__init__.py 259s pysam 0.23.0 /usr/lib/python3/dist-packages/pysam/__init__.py 259s 259s Python packages OK: True 259s 259s Everything looks OK: True 259s Temporary directory: /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i 259s ______________________ Mapping reads to clustered genes _______________________ 259s Finished mapping 259s 259s _____________________________ Generating clusters _____________________________ 259s syscall: sort -k1,1 -k 2,2n /tmp/tmp.5Pqo1iqXhC/foo/OUT/minimap.reads > /tmp/tmp.5Pqo1iqXhC/foo/OUT/read_store 259s Compressing file /tmp/tmp.5Pqo1iqXhC/foo/OUT/read_store 259s Found 51 proper read pairs from minimap 259s Total clusters to perform local assemblies: 9 259s 259s Insert size information from reads mapped to reference genes: 259s Insert size: 185.0 259s Insert sspace sd: 0.27 259s Max insert: 220.55 259s 259s ___________________________ Assembling each cluster ___________________________ 259s Will run 1 cluster(s) in parallel 259s Not constructing cluster cluster because it only has 2 reads (1 of 9) 259s Constructing cluster cluster_1 (2 of 9) 259s Constructing cluster cluster_2 (3 of 9) 259s Constructing cluster cluster_3 (4 of 9) 259s Constructing cluster cluster_4 (5 of 9) 259s Constructing cluster gene (6 of 9) 259s Constructing cluster gene_1 (7 of 9) 259s Constructing cluster noncoding (8 of 9) 259s Constructing cluster noncoding_1 (9 of 9) 259s Start running cluster cluster_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_1 261s cluster_1 detected 1 threads available to it 261s cluster_1 reported completion 261s Finished running cluster cluster_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_1 261s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_1 261s Start running cluster cluster_2 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_2 263s cluster_2 detected 1 threads available to it 263s cluster_2 reported completion 263s Finished running cluster cluster_2 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_2 263s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_2 263s Start running cluster cluster_3 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_3 265s cluster_3 detected 1 threads available to it 265s cluster_3 reported completion 265s Finished running cluster cluster_3 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_3 265s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_3 265s Start running cluster cluster_4 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_4 266s cluster_4 detected 1 threads available to it 266s cluster_4 reported completion 266s Finished running cluster cluster_4 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_4 266s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/cluster_4 266s Start running cluster gene in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene 268s gene detected 1 threads available to it 268s gene reported completion 268s Finished running cluster gene in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene 268s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene 268s Start running cluster gene_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene_1 270s gene_1 detected 1 threads available to it 270s gene_1 reported completion 270s Finished running cluster gene_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene_1 270s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/gene_1 270s Start running cluster noncoding in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding 272s noncoding detected 1 threads available to it 272s noncoding reported completion 272s Finished running cluster noncoding in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding 272s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding 272s Start running cluster noncoding_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding_1 273s noncoding_1 detected 1 threads available to it 273s noncoding_1 reported completion 273s Finished running cluster noncoding_1 in directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding_1 273s Deleting cluster dir /tmp/tmp.5Pqo1iqXhC/foo/OUT/ariba.tmp.eiys1m0i/noncoding_1 274s Final value of remaining_clusters counter: Value('l', 0) 274s Finished assembling clusters 274s 274s _______________________________ Writing reports _______________________________ 274s Making /tmp/tmp.5Pqo1iqXhC/foo/OUT/debug.report.tsv 274s Making /tmp/tmp.5Pqo1iqXhC/foo/OUT/report.tsv 274s 274s ____________________ Writing fasta of assembled sequences _____________________ 274s /tmp/tmp.5Pqo1iqXhC/foo/OUT/assembled_seqs.fa.gz and /tmp/tmp.5Pqo1iqXhC/foo/OUT/assembled_genes.fa.gz 274s 274s __________________________ Catting cluster log files __________________________ 274s Writing file /tmp/tmp.5Pqo1iqXhC/foo/OUT/log.clusters.gz 274s 274s _______________________________ Cleaning files ________________________________ 274s Deleting Logs directory /tmp/tmp.5Pqo1iqXhC/foo/OUT/Logs 274s Deleting reads store files /tmp/tmp.5Pqo1iqXhC/foo/OUT/read_store.gz[.tbi] 274s 274s All done! 274s 274s Running ARIBA on test data... 274s ------------------------------------------------------------------------------- 274s |=============================================================================| 274s | Preparing input data | 274s |=============================================================================| 274s ------------------------------------------------------------------------------- 274s Made output directory ./foo. Copying test data files into it: 274s copied ref_seqs.fa 274s copied metadata.tsv 274s copied reads_1.fq 274s copied reads_2.fq 274s ------------------------------------------------------------------------------- 274s |=============================================================================| 274s | Try running ariba prepareref | 274s |=============================================================================| 274s ------------------------------------------------------------------------------- 274s 274s Running ariba prepareref with: 274s /usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF 274s 274s 274s ariba prepareref finished OK 274s ------------------------------------------------------------------------------- 274s |=============================================================================| 274s | Try running ariba run | 274s |=============================================================================| 274s ------------------------------------------------------------------------------- 274s 274s Running ARIBA with: 274s /usr/bin/ariba run --verbose --threads 1 PREPAREREF reads_1.fq reads_2.fq OUT 274s 274s 274s ariba run finished OK 274s Finished run on test data OK 274s autopkgtest [19:25:31]: test test-example: -----------------------] 275s test-example PASS 275s autopkgtest [19:25:32]: test test-example: - - - - - - - - - - results - - - - - - - - - - 276s autopkgtest [19:25:33]: @@@@@@@@@@@@@@@@@@@@ summary 276s test-example PASS 301s nova [W] Using flock in prodstack6-arm64 301s flock: timeout while waiting to get lock 301s Creating nova instance adt-plucky-arm64-ariba-20250306-192056-juju-7f2275-prod-proposed-migration-environment-2-fad496ee-b96c-40b2-8d27-240930a6ed95 from image adt/ubuntu-plucky-arm64-server-20250306.img (UUID f19aab3f-524b-4043-adcc-51a09d4a0883)... 301s nova [W] Timed out waiting for 70f25087-0060-4228-b60a-77f46109da57 to get deleted.