0s autopkgtest [01:29:07]: starting date and time: 2025-03-16 01:29:07+0000 0s autopkgtest [01:29:07]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:29:07]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.75rwo074/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:scikit-learn --apt-upgrade mcaller --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- lxd -r lxd-armhf-10.145.243.46 lxd-armhf-10.145.243.46:autopkgtest/ubuntu/plucky/armhf 32s autopkgtest [01:29:39]: testbed dpkg architecture: armhf 34s autopkgtest [01:29:41]: testbed apt version: 2.9.33 38s autopkgtest [01:29:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s autopkgtest [01:29:46]: testbed release detected to be: None 47s autopkgtest [01:29:54]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 50s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 50s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 50s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 50s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [74.9 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1792 B] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [290 kB] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [10.5 kB] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4168 B] 51s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 51s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1389 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 53s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 79s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 80s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.5 kB] 80s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 80s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.3 MB] 99s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 102s Fetched 41.1 MB in 52s (794 kB/s) 102s Reading package lists... 108s autopkgtest [01:30:55]: upgrading testbed (apt dist-upgrade and autopurge) 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 112s Entering ResolveByKeep 113s 113s Calculating upgrade... 114s The following packages will be upgraded: 114s pinentry-curses python3-jinja2 sos strace 114s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 960 kB of archives. 114s After this operation, 23.6 kB of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 116s Fetched 960 kB in 2s (632 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 ... 64655 files and directories currently installed.) 116s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 116s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 116s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 116s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 116s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 116s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 116s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 116s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 117s Setting up sos (4.9.0-5) ... 117s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 117s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 118s Setting up strace (6.13+ds-1ubuntu1) ... 118s Processing triggers for man-db (2.13.0-1) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 122s Starting 2 pkgProblemResolver with broken count: 0 122s Done 122s Solving dependencies... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [01:31:12]: rebooting testbed after setup commands that affected boot 166s autopkgtest [01:31:53]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 191s autopkgtest [01:32:18]: @@@@@@@@@@@@@@@@@@@@ apt-source mcaller 205s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mcaller 1.0.3+git20210624.b415090-3 (dsc) [2372 B] 205s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mcaller 1.0.3+git20210624.b415090-3 (tar) [6613 kB] 205s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mcaller 1.0.3+git20210624.b415090-3 (diff) [7488 B] 206s gpgv: Signature made Wed Apr 27 22:26:52 2022 UTC 206s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 206s gpgv: issuer "emollier@debian.org" 206s gpgv: Can't check signature: No public key 206s dpkg-source: warning: cannot verify inline signature for ./mcaller_1.0.3+git20210624.b415090-3.dsc: no acceptable signature found 206s autopkgtest [01:32:33]: testing package mcaller version 1.0.3+git20210624.b415090-3 208s autopkgtest [01:32:35]: build not needed 211s autopkgtest [01:32:38]: test run-unit-test: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 215s The following NEW packages will be installed: 215s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 215s fonts-urw-base35 libaec0 libblas3 libcairo2 libdeflate0 libfontconfig1 215s libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b 215s libhdf5-310 libhdf5-hl-310 libhts3t64 libhtscodecs2 libimagequant0 libjbig0 215s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 215s liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libpixman-1-0 libqhull-r8.0 215s libraqm0 libsharpyuv0 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 215s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 215s libxslt1.1 libxss1 mcaller python-matplotlib-data python3-biopython 215s python3-brotli python3-cairo python3-contourpy python3-cycler 215s python3-decorator python3-fonttools python3-freetype python3-fs python3-h5py 215s python3-h5py-serial python3-joblib python3-kiwisolver python3-lxml 215s python3-lz4 python3-matplotlib python3-mpmath python3-numpy 215s python3-numpy-dev python3-pandas python3-pandas-lib python3-pil 215s python3-pil.imagetk python3-platformdirs python3-pysam python3-pytz 215s python3-reportlab python3-rlpycairo python3-scipy python3-seaborn 215s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 215s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 215s python3.13-tk sgml-base tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common 215s xfonts-encodings xfonts-utils xml-core 215s 0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 106 MB of archives. 215s After this operation, 412 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 215s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 215s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 215s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 217s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 219s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sgml-base all 1.31 [11.4 kB] 219s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 220s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 220s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 220s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 221s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libfontenc1 armhf 1:1.1.8-1build1 [11.5 kB] 221s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 221s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 221s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf xfonts-utils armhf 1:7.7+7 [90.6 kB] 221s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-urw-base35 all 20200910-8 [11.0 MB] 228s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 228s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 228s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 228s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 228s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 228s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 229s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-8 [527 kB] 229s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf blt armhf 2.5.3+dfsg-8 [4824 B] 229s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-lyx all 2.4.3-1 [171 kB] 229s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 229s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 229s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 229s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 229s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 229s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 229s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 229s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 229s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 230s Get:34 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 230s Get:35 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 231s Get:36 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 231s Get:37 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 231s Get:38 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 231s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libimagequant0 armhf 2.18.0-1build1 [31.1 kB] 231s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 231s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 231s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 232s Get:43 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 232s Get:44 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 232s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf liblcms2-2 armhf 2.16-2 [137 kB] 232s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 232s Get:47 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 232s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf libqhull-r8.0 armhf 2020.2-6build1 [173 kB] 232s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libraqm0 armhf 0.10.2-1 [12.4 kB] 232s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 232s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 232s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 232s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 232s Get:54 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpdemux2 armhf 1.5.0-0.1 [11.5 kB] 232s Get:55 http://ftpmaster.internal/ubuntu plucky/main armhf libwebpmux3 armhf 1.5.0-0.1 [22.4 kB] 232s Get:56 http://ftpmaster.internal/ubuntu plucky/main armhf libxslt1.1 armhf 1.1.39-0exp1ubuntu2 [152 kB] 232s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.4.2-3 [205 kB] 233s Get:58 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 233s Get:59 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu2 [16.7 MB] 245s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 245s Get:61 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-8 [4014 kB] 248s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 250s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.13.0-1 [1113 kB] 251s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.13.0-1 [7978 B] 251s Get:65 http://ftpmaster.internal/ubuntu plucky/main armhf python3.12-tk armhf 3.12.9-1 [113 kB] 251s Get:66 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-tk armhf 3.13.2-2 [103 kB] 251s Get:67 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tk armhf 3.13.1-1 [9770 B] 251s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pil.imagetk armhf 11.1.0-5build1 [9226 B] 251s Get:69 http://ftpmaster.internal/ubuntu plucky/main armhf libopenjp2-7 armhf 2.5.3-2 [172 kB] 251s Get:70 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pil armhf 11.1.0-5build1 [435 kB] 251s Get:71 http://ftpmaster.internal/ubuntu plucky/main armhf python3-cairo armhf 1.26.1-2build2 [114 kB] 251s Get:72 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-freetype all 2.5.1-1 [92.3 kB] 251s Get:73 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-rlpycairo all 0.3.0-3 [9130 B] 251s Get:74 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-reportlab all 4.3.1-1 [1137 kB] 252s Get:75 http://ftpmaster.internal/ubuntu plucky/main armhf xml-core all 0.19 [20.3 kB] 252s Get:76 http://ftpmaster.internal/ubuntu plucky/universe armhf w3c-sgml-lib all 1.3-3 [280 kB] 252s Get:77 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biopython armhf 1.85+dfsg-2build1 [1692 kB] 253s Get:78 http://ftpmaster.internal/ubuntu plucky/universe armhf python-matplotlib-data all 3.8.3-7build1 [2934 kB] 255s Get:79 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-contourpy armhf 1.3.1-1build1 [195 kB] 255s Get:80 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-cycler all 0.12.1-1 [9716 B] 255s Get:81 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-brotli armhf 1.1.0-2build4 [322 kB] 255s Get:82 http://ftpmaster.internal/ubuntu plucky/main armhf python3-platformdirs all 4.3.6-1 [16.8 kB] 255s Get:83 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fs all 2.4.16-7 [90.8 kB] 255s Get:84 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lxml armhf 5.3.1-1build1 [1282 kB] 256s Get:85 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-lz4 armhf 4.4.0+dfsg-1build1 [25.3 kB] 256s Get:86 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-mpmath all 1.3.0-1 [425 kB] 256s Get:87 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-sympy all 1.13.3-5 [4229 kB] 259s Get:88 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 259s Get:89 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-unicodedata2 armhf 15.1.0+ds-1build3 [357 kB] 259s Get:90 http://ftpmaster.internal/ubuntu plucky/universe armhf unicode-data all 15.1.0-1 [8878 kB] 264s Get:91 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-fonttools armhf 4.55.3-2build1 [1462 kB] 265s Get:92 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-kiwisolver armhf 1.4.7-3build1 [57.7 kB] 265s Get:93 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-matplotlib armhf 3.8.3-7build1 [17.3 MB] 275s Get:94 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pytz all 2025.1-3 [162 kB] 276s Get:95 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2025.1-3 [1866 B] 276s Get:96 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-8build1 [4877 kB] 278s Get:97 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 280s Get:98 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-seaborn all 0.13.2-4.1 [225 kB] 280s Get:99 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pysam armhf 0.23.0+ds-1build1 [3569 kB] 283s Get:100 http://ftpmaster.internal/ubuntu plucky/universe armhf mcaller all 1.0.3+git20210624.b415090-3 [19.3 kB] 283s Fetched 106 MB in 1min 8s (1554 kB/s) 283s Selecting previously unselected package python3-numpy-dev:armhf. 283s (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 ... 64655 files and directories currently installed.) 283s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 283s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 283s Selecting previously unselected package libblas3:armhf. 283s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 283s Unpacking libblas3:armhf (3.12.1-2) ... 283s Selecting previously unselected package libgfortran5:armhf. 284s Preparing to unpack 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284s Selecting previously unselected package fonts-dejavu-mono. 284s Preparing to unpack .../08-fonts-dejavu-mono_2.37-8_all.deb ... 284s Unpacking fonts-dejavu-mono (2.37-8) ... 284s Selecting previously unselected package fonts-dejavu-core. 284s Preparing to unpack .../09-fonts-dejavu-core_2.37-8_all.deb ... 284s Unpacking fonts-dejavu-core (2.37-8) ... 284s Selecting previously unselected package libfontenc1:armhf. 284s Preparing to unpack .../10-libfontenc1_1%3a1.1.8-1build1_armhf.deb ... 284s Unpacking libfontenc1:armhf (1:1.1.8-1build1) ... 284s Selecting previously unselected package x11-common. 284s Preparing to unpack .../11-x11-common_1%3a7.7+23ubuntu3_all.deb ... 284s Unpacking x11-common (1:7.7+23ubuntu3) ... 284s Selecting previously unselected package xfonts-encodings. 284s Preparing to unpack .../12-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 284s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 285s Selecting previously unselected package xfonts-utils. 285s 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.../18-libxft2_2.3.6-1build1_armhf.deb ... 285s Unpacking libxft2:armhf (2.3.6-1build1) ... 285s Selecting previously unselected package libxss1:armhf. 285s Preparing to unpack .../19-libxss1_1%3a1.2.3-1build3_armhf.deb ... 285s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 286s Selecting previously unselected package libtk8.6:armhf. 286s Preparing to unpack .../20-libtk8.6_8.6.16-1_armhf.deb ... 286s Unpacking libtk8.6:armhf (8.6.16-1) ... 286s Selecting previously unselected package tk8.6-blt2.5. 286s Preparing to unpack .../21-tk8.6-blt2.5_2.5.3+dfsg-8_armhf.deb ... 286s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 286s Selecting previously unselected package blt. 286s Preparing to unpack .../22-blt_2.5.3+dfsg-8_armhf.deb ... 286s Unpacking blt (2.5.3+dfsg-8) ... 286s Selecting previously unselected package fonts-lyx. 286s Preparing to unpack .../23-fonts-lyx_2.4.3-1_all.deb ... 286s Unpacking fonts-lyx (2.4.3-1) ... 286s Selecting previously unselected package libaec0:armhf. 286s 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286s Selecting previously unselected package libgomp1:armhf. 286s Preparing to unpack .../30-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 286s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 286s Selecting previously unselected package libgraphite2-3:armhf. 286s Preparing to unpack .../31-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 286s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 286s Selecting previously unselected package libharfbuzz0b:armhf. 286s Preparing to unpack .../32-libharfbuzz0b_10.2.0-1_armhf.deb ... 286s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 286s Selecting previously unselected package libsz2:armhf. 286s Preparing to unpack .../33-libsz2_1.1.3-1_armhf.deb ... 286s Unpacking libsz2:armhf (1.1.3-1) ... 286s Selecting previously unselected package libhdf5-310:armhf. 286s Preparing to unpack .../34-libhdf5-310_1.14.5+repack-3_armhf.deb ... 286s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 286s Selecting previously unselected package libhdf5-hl-310:armhf. 286s Preparing to unpack .../35-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 286s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 286s Selecting previously unselected package libhtscodecs2:armhf. 286s Preparing to unpack .../36-libhtscodecs2_1.6.1-2_armhf.deb ... 286s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 287s Selecting previously unselected package libhts3t64:armhf. 287s Preparing to unpack .../37-libhts3t64_1.21+ds-1_armhf.deb ... 287s Unpacking libhts3t64:armhf (1.21+ds-1) ... 287s Selecting previously unselected package libimagequant0:armhf. 287s Preparing to unpack .../38-libimagequant0_2.18.0-1build1_armhf.deb ... 287s Unpacking libimagequant0:armhf (2.18.0-1build1) ... 287s Selecting previously unselected package libjpeg-turbo8:armhf. 287s Preparing to unpack .../39-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 287s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 287s Selecting previously unselected package libjpeg8:armhf. 287s Preparing to unpack .../40-libjpeg8_8c-2ubuntu11_armhf.deb ... 287s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 287s Selecting previously unselected package libjs-jquery. 287s Preparing to unpack .../41-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 287s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 287s Selecting previously unselected package libjs-jquery-ui. 287s Preparing to unpack .../42-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 287s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 287s Selecting previously unselected package liblbfgsb0:armhf. 287s Preparing to unpack .../43-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 287s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 287s Selecting previously unselected package liblcms2-2:armhf. 287s Preparing to unpack .../44-liblcms2-2_2.16-2_armhf.deb ... 287s Unpacking liblcms2-2:armhf (2.16-2) ... 287s Selecting previously unselected package liblerc4:armhf. 287s Preparing to unpack .../45-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 287s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 287s Selecting previously unselected package liblzf1:armhf. 287s Preparing to unpack .../46-liblzf1_3.6-4_armhf.deb ... 287s Unpacking liblzf1:armhf (3.6-4) ... 287s Selecting previously unselected package libqhull-r8.0:armhf. 287s Preparing to unpack .../47-libqhull-r8.0_2020.2-6build1_armhf.deb ... 287s Unpacking libqhull-r8.0:armhf (2020.2-6build1) ... 287s Selecting previously unselected package libraqm0:armhf. 287s Preparing to unpack .../48-libraqm0_0.10.2-1_armhf.deb ... 287s Unpacking libraqm0:armhf (0.10.2-1) ... 287s Selecting previously unselected package libsharpyuv0:armhf. 287s Preparing to unpack .../49-libsharpyuv0_1.5.0-0.1_armhf.deb ... 287s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 287s Selecting previously unselected package libjbig0:armhf. 287s Preparing to unpack .../50-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 287s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 287s Selecting previously unselected package libwebp7:armhf. 287s 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python3-rlpycairo (0.3.0-3) ... 290s Selecting previously unselected package python3-reportlab. 290s Preparing to unpack .../73-python3-reportlab_4.3.1-1_all.deb ... 290s Unpacking python3-reportlab (4.3.1-1) ... 290s Selecting previously unselected package xml-core. 290s Preparing to unpack .../74-xml-core_0.19_all.deb ... 290s Unpacking xml-core (0.19) ... 290s Selecting previously unselected package w3c-sgml-lib. 290s Preparing to unpack .../75-w3c-sgml-lib_1.3-3_all.deb ... 290s Unpacking w3c-sgml-lib (1.3-3) ... 290s Selecting previously unselected package python3-biopython. 290s Preparing to unpack .../76-python3-biopython_1.85+dfsg-2build1_armhf.deb ... 290s Unpacking python3-biopython (1.85+dfsg-2build1) ... 290s Selecting previously unselected package python-matplotlib-data. 290s Preparing to unpack .../77-python-matplotlib-data_3.8.3-7build1_all.deb ... 290s Unpacking python-matplotlib-data (3.8.3-7build1) ... 290s Selecting previously unselected package python3-contourpy. 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python3-lxml:armhf (5.3.1-1build1) ... 291s Selecting previously unselected package python3-lz4. 291s Preparing to unpack .../84-python3-lz4_4.4.0+dfsg-1build1_armhf.deb ... 291s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 291s Selecting previously unselected package python3-mpmath. 291s Preparing to unpack .../85-python3-mpmath_1.3.0-1_all.deb ... 291s Unpacking python3-mpmath (1.3.0-1) ... 291s Selecting previously unselected package python3-sympy. 291s Preparing to unpack .../86-python3-sympy_1.13.3-5_all.deb ... 291s Unpacking python3-sympy (1.13.3-5) ... 292s Selecting previously unselected package python3-ufolib2. 292s Preparing to unpack .../87-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 292s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 292s Selecting previously unselected package python3-unicodedata2. 292s Preparing to unpack .../88-python3-unicodedata2_15.1.0+ds-1build3_armhf.deb ... 292s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 292s Selecting previously unselected package unicode-data. 292s Preparing to unpack .../89-unicode-data_15.1.0-1_all.deb ... 292s Unpacking unicode-data (15.1.0-1) ... 292s Selecting previously unselected package python3-fonttools. 292s Preparing to unpack .../90-python3-fonttools_4.55.3-2build1_armhf.deb ... 292s Unpacking python3-fonttools (4.55.3-2build1) ... 292s Selecting previously unselected package python3-kiwisolver. 292s Preparing to unpack .../91-python3-kiwisolver_1.4.7-3build1_armhf.deb ... 292s Unpacking python3-kiwisolver (1.4.7-3build1) ... 292s Selecting previously unselected package python3-matplotlib. 292s Preparing to unpack .../92-python3-matplotlib_3.8.3-7build1_armhf.deb ... 292s Unpacking python3-matplotlib (3.8.3-7build1) ... 293s Selecting previously unselected package python3-pytz. 293s Preparing to unpack .../93-python3-pytz_2025.1-3_all.deb ... 293s Unpacking python3-pytz (2025.1-3) ... 293s Selecting previously unselected package python3-tz. 293s Preparing to unpack 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294s Unpacking mcaller (1.0.3+git20210624.b415090-3) ... 294s Setting up libhtscodecs2:armhf (1.6.1-2) ... 294s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 294s Setting up liblcms2-2:armhf (2.16-2) ... 294s Setting up libpixman-1-0:armhf (0.44.0-3) ... 294s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 294s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 294s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 294s Setting up python3-joblib (1.4.2-3) ... 295s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 295s Setting up libxcb-render0:armhf (1.17.0-2) ... 295s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 295s Setting up fonts-lyx (2.4.3-1) ... 295s Setting up python3-threadpoolctl (3.1.0-1) ... 295s Setting up x11-common (1:7.7+23ubuntu3) ... 295s Setting up libdeflate0:armhf (1.23-1) ... 295s Setting up libqhull-r8.0:armhf (2020.2-6build1) ... 295s Setting up python3-pytz (2025.1-3) ... 296s Setting up libxcb-shm0:armhf (1.17.0-2) ... 296s Setting up 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python3-sympy (1.13.3-5) ... 305s Setting up liblapack3:armhf (3.12.1-2) ... 305s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 305s Setting up python3-pysam (0.23.0+ds-1build1) ... 305s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 306s Setting up libwebpdemux2:armhf (1.5.0-0.1) ... 306s Setting up python3-freetype (2.5.1-1) ... 306s Setting up xfonts-utils (1:7.7+7) ... 306s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 306s Setting up libraqm0:armhf (0.10.2-1) ... 306s Setting up python3-numpy (1:2.2.3+ds-5) ... 308s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 308s Setting up python3-lxml:armhf (5.3.1-1build1) ... 308s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu4) ... 308s Setting up xml-core (0.19) ... 308s Setting up python3-contourpy (1.3.1-1build1) ... 309s Setting up libfontconfig1:armhf (2.15.0-2ubuntu1) ... 309s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 309s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 309s Setting up libxft2:armhf (2.3.6-1build1) ... 309s Setting up python3-scipy (1.14.1-4ubuntu2) ... 312s Setting up libtk8.6:armhf (8.6.16-1) ... 312s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-8build1) ... 312s Setting up python3.12-tk (3.12.9-1) ... 313s Setting up python3-sklearn-lib:armhf (1.4.2+dfsg-8) ... 313s Setting up python3-h5py-serial (3.13.0-1) ... 313s Setting up fonts-urw-base35 (20200910-8) ... 313s Setting up libcairo2:armhf (1.18.2-2) ... 313s Setting up python3.13-tk (3.13.2-2) ... 313s Setting up python3-pil:armhf (11.1.0-5build1) ... 314s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 322s Setting up python3-h5py (3.13.0-1) ... 322s Setting up python3-sklearn (1.4.2+dfsg-8) ... 324s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 324s Setting up python3-cairo (1.26.1-2build2) ... 325s Setting up blt (2.5.3+dfsg-8) ... 325s Setting up python3-tk:armhf (3.13.1-1) ... 325s Setting up python3-pil.imagetk:armhf (11.1.0-5build1) ... 325s Setting up python3-rlpycairo (0.3.0-3) ... 325s Setting up python3-reportlab (4.3.1-1) ... 326s Setting up python3-fonttools (4.55.3-2build1) ... 327s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 327s Setting up python3-matplotlib (3.8.3-7build1) ... 329s Setting up python3-seaborn (0.13.2-4.1) ... 329s Processing triggers for man-db (2.13.0-1) ... 330s Processing triggers for libc-bin (2.41-1ubuntu1) ... 331s Processing triggers for sgml-base (1.31) ... 331s Setting up w3c-sgml-lib (1.3-3) ... 368s Setting up python3-biopython (1.85+dfsg-2build1) ... 370s Setting up mcaller (1.0.3+git20210624.b415090-3) ... 384s autopkgtest [01:35:31]: test run-unit-test: [----------------------- 388s testdata/ 388s 1 contigs 388s 1 threads 388s thread finished processing...: 388s 35 observations 388s 35 positions 388s 0 regions with multiple methylated bases 388s 0 observations with skips included 388s 8 observations with too many skips 388s Finished extracting signals 390s testdata/ 390s 1 contigs 390s 1 threads 390s thread finished processing...: 390s 9 observations 390s 9 positions 390s 0 regions with multiple methylated bases 390s 0 observations with skips included 390s 2 observations with too many skips 390s Finished extracting signals 391s testdata/ 391s 1 contigs 391s 4 threads 392s Error: could not find sequence for reference contig li 392s thread finished processing...: 392s 16 observations 392s 16 positions 392s 0 regions with multiple methylated bases 392s 0 observations with skips included 392s 6 observations with too many skips 392s thread finished processing...: 392s 28 observations 392s 28 positions 392s 0 regions with multiple methylated bases 392s 0 observations with skips included 392s 6 observations with too many skips 392s thread finished processing...: 392s 9 observations 392s 9 positions 392s 0 regions with multiple methylated bases 392s 0 observations with skips included 392s 4 observations with too many skips 392s thread finished processing...: 392s 44 observations 392s 44 positions 392s 1 regions with multiple methylated bases 392s 0 observations with skips included 392s 10 observations with too many skips 393s Finished extracting signals 393s Merging files... 393s Training... 393s ['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'] 393s [[np.float64(-2.15), np.float64(1.8849999999999998), np.float64(2.58), np.float64(-0.36), np.float64(4.26), np.float64(-2.4625), np.float64(7.055265349382997)], [np.float64(1.485), np.float64(4.095000000000001), np.float64(-1.12), np.float64(-0.91), np.float64(-0.62), np.float64(1.17), np.float64(7.055265349382997)], [np.float64(1.095), np.float64(0.78), np.float64(-2.38), np.float64(1.47), np.float64(-1.7149999999999999), np.float64(-0.8283333333333335), np.float64(7.055265349382997)], [np.float64(-3.59), np.float64(1.8566666666666667), np.float64(-0.9600000000000001), np.float64(0.06714285714285717), np.float64(0.5733333333333334), np.float64(1.21), np.float64(7.055265349382997)], [np.float64(1.0050000000000001), np.float64(3.05), np.float64(3.07), np.float64(0.46249999999999997), np.float64(0.32), np.float64(-0.6033333333333334), np.float64(7.055265349382997)], [np.float64(-0.18999999999999992), np.float64(-1.6799999999999997), np.float64(-2.3), np.float64(0.56), np.float64(-1.41), np.float64(1.48), np.float64(7.055265349382997)], [np.float64(-1.1300000000000001), np.float64(-1.67), np.float64(-1.1), np.float64(-0.5774999999999999), np.float64(0.42), np.float64(1.0225), np.float64(7.055265349382997)], [np.float64(0.0050000000000000044), np.float64(-0.29500000000000004), np.float64(-0.54), np.float64(3.96), np.float64(1.47), np.float64(0.06499999999999995), np.float64(7.055265349382997)], [np.float64(3.255), np.float64(3.925), np.float64(0.03999999999999998), np.float64(-0.15599999999999997), np.float64(-1.01), np.float64(1.3533333333333333), np.float64(7.055265349382997)], [np.float64(-0.07999999999999996), np.float64(-1.3666666666666665), np.float64(0.84), np.float64(-0.5449999999999999), np.float64(-3.22), np.float64(-1.53), np.float64(7.055265349382997)]] 393s ['AGGCCMTTCAA', 'AATCAMAAGAA', 'TACTTMCCGCA', 'AACTCMAGGTA', 'GAAGAMTCAAC', 'GGATTMTTTCA', 'CTGGAMAAAGC', 'GGGCCMTTACC', 'GGTGGMTGAAT', 'GGTTAMCGCGT'] 393s NN general model scores: 0.875,1.0,0.375,0.875,0.5 393s Cross validation accuracy: 0.72 (+/- 0.48) 393s Finished training 393s PASS 393s autopkgtest [01:35:40]: test run-unit-test: -----------------------] 397s run-unit-test PASS 397s autopkgtest [01:35:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 401s autopkgtest [01:35:48]: @@@@@@@@@@@@@@@@@@@@ summary 401s run-unit-test PASS