0s autopkgtest [12:24:13]: starting date and time: 2024-11-13 12:24:13+0000 0s autopkgtest [12:24:13]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [12:24:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ig_n6irc/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-2.secgroup --name adt-plucky-i386-cnvkit-20241113-122413-juju-7f2275-prod-proposed-migration-environment-2-cc351134-859e-4525-8038-108608b1b304 --image adt/ubuntu-plucky-amd64-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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 67s autopkgtest [12:25:20]: testbed dpkg architecture: amd64 71s autopkgtest [12:25:24]: testbed apt version: 2.9.8 75s autopkgtest [12:25:28]: test architecture: i386 75s autopkgtest [12:25:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.6 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [131 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [721 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [281 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.3 kB] 77s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [38.5 kB] 77s Fetched 2466 kB in 0s (6890 kB/s) 77s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s The following NEW packages will be installed: 97s python3.13-gdbm 97s The following packages will be upgraded: 97s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 97s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 253 kB of archives. 97s After this operation, 147 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 97s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 97s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 97s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 98s Fetched 253 kB in 0s (9778 kB/s) 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 98s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 98s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 98s Setting up python3-minimal (3.12.7-1) ... 98s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 98s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 98s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 98s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 98s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 98s Selecting previously unselected package python3.13-gdbm. 98s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 98s Unpacking python3.13-gdbm (3.13.0-2) ... 98s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 98s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 98s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 98s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 98s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 98s Setting up python3.13-gdbm (3.13.0-2) ... 98s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 98s Setting up python3 (3.12.7-1) ... 99s Setting up python3-gdbm:amd64 (3.12.7-1) ... 99s Processing triggers for man-db (2.12.1-3) ... 99s Processing triggers for libc-bin (2.40-1ubuntu3) ... 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 100s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 100s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 100s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 101s Reading package lists... 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [12:26:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 129s autopkgtest [12:26:22]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 139s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (dsc) [2449 B] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (tar) [23.7 MB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (diff) [17.7 kB] 139s gpgv: Signature made Mon Apr 8 08:42:55 2024 UTC 139s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found 140s autopkgtest [12:26:33]: testing package cnvkit version 0.9.10-2 146s autopkgtest [12:26:39]: build not needed 155s autopkgtest [12:26:48]: test run-unit-test: preparing testbed 171s Note, using file '/tmp/autopkgtest.lQrRjI/1-autopkgtest-satdep.dsc' to get the build dependencies 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 173s The following NEW packages will be installed: 173s blt build-essential cnvkit cpp cpp-14 cpp-14-x86-64-linux-gnu 173s cpp-x86-64-linux-gnu fontconfig fontconfig-config fonts-dejavu-core 173s fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-14 173s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 173s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libblas3 libcairo2 173s libcc1-0 libdatrie1 libdeflate0 libfontconfig1 libfontenc1 libgcc-14-dev 173s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 173s libhwasan0 libice6 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 173s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 173s liblerc4 liblsan0 libmpc3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 173s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 173s libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libsm6 libstdc++-14-dev 173s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 173s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 173s libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 173s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 173s python3-cairo python3-contourpy python3-cycler python3-dateutil 173s python3-decorator python3-fonttools python3-freetype python3-fs 173s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 173s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 173s python3-packaging python3-pandas python3-pandas-lib python3-pil 173s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 173s python3-reportlab python3-rlpycairo python3-scipy python3-six 173s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 173s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 173s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 173s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 173s xfonts-encodings xfonts-utils xml-core zip 176s 0 upgraded, 141 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 227 MB of archives. 176s After this operation, 903 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 176s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 176s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 176s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 176s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 176s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 176s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 176s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 176s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 176s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 176s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 176s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 176s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 176s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 176s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 176s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 176s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 176s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 176s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 176s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 176s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 176s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 176s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 176s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 176s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 176s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 176s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 176s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 176s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 176s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 176s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 176s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 176s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 176s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 176s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 176s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 176s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 176s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 176s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 176s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 176s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 176s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 176s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 176s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 176s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 176s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 176s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 176s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 176s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 176s Get:50 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 176s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 176s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 176s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 176s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 176s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 176s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 176s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 176s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 176s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 176s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 176s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 176s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 176s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 176s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 176s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 176s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 176s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 176s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 176s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 176s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 176s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 176s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 176s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 176s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 176s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 176s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 176s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 176s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 176s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 176s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 176s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 176s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 176s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 176s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 176s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 176s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 176s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 176s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 176s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 176s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 176s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 176s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 176s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 176s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 176s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 176s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 176s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 176s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 176s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 176s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 176s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 176s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 176s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 176s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 176s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 176s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 176s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 176s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 176s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 176s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 176s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 176s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.14.8-6 [2549 kB] 176s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 176s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 176s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 176s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 176s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 176s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 176s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 176s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 176s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu1 [185 kB] 176s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 176s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 176s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 176s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 176s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 176s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 176s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 176s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 176s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 176s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 176s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 176s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 176s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 176s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 176s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1 [28.9 MB] 176s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.50.0-2 [605 kB] 176s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.78.0-1 [378 kB] 176s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.10-2 [20.5 MB] 176s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler140 amd64 24.08.0-1 [1168 kB] 176s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 24.08.0-1 [225 kB] 177s Preconfiguring packages ... 177s Fetched 227 MB in 3s (80.9 MB/s) 177s Selecting previously unselected package sgml-base. 177s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 177s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 177s Unpacking sgml-base (1.31) ... 177s Selecting previously unselected package libtcl8.6:amd64. 177s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 177s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 177s Selecting previously unselected package fonts-dejavu-mono. 177s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 177s Unpacking fonts-dejavu-mono (2.37-8) ... 177s Selecting previously unselected package fonts-dejavu-core. 177s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 177s Unpacking fonts-dejavu-core (2.37-8) ... 177s Selecting previously unselected package libfontenc1:amd64. 177s Preparing to unpack .../004-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 177s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 177s Selecting previously unselected package x11-common. 177s Preparing to unpack .../005-x11-common_1%3a7.7+23ubuntu3_all.deb ... 177s Unpacking x11-common (1:7.7+23ubuntu3) ... 177s Selecting previously unselected package xfonts-encodings. 177s Preparing to unpack .../006-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 177s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 177s Selecting previously unselected package xfonts-utils. 177s Preparing to unpack .../007-xfonts-utils_1%3a7.7+7_amd64.deb ... 177s Unpacking xfonts-utils (1:7.7+7) ... 177s Selecting previously unselected package fonts-urw-base35. 177s Preparing to unpack .../008-fonts-urw-base35_20200910-8_all.deb ... 177s Unpacking fonts-urw-base35 (20200910-8) ... 177s Selecting previously unselected package fontconfig-config. 177s Preparing to unpack .../009-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 178s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 178s Selecting previously unselected package libfontconfig1:amd64. 178s Preparing to unpack .../010-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 178s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 178s Selecting previously unselected package libxrender1:amd64. 178s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 178s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 178s Selecting previously unselected package libxft2:amd64. 178s Preparing to unpack .../012-libxft2_2.3.6-1build1_amd64.deb ... 178s Unpacking libxft2:amd64 (2.3.6-1build1) ... 178s Selecting previously unselected package libxss1:amd64. 178s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 178s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 178s Selecting previously unselected package libtk8.6:amd64. 178s Preparing to unpack .../014-libtk8.6_8.6.15-1_amd64.deb ... 178s Unpacking libtk8.6:amd64 (8.6.15-1) ... 178s Selecting previously unselected package tk8.6-blt2.5. 178s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 178s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 178s Selecting previously unselected package blt. 178s Preparing to unpack .../016-blt_2.5.3+dfsg-7build1_amd64.deb ... 178s Unpacking blt (2.5.3+dfsg-7build1) ... 178s Selecting previously unselected package libisl23:amd64. 178s Preparing to unpack .../017-libisl23_0.27-1_amd64.deb ... 178s Unpacking libisl23:amd64 (0.27-1) ... 178s Selecting previously unselected package libmpc3:amd64. 178s Preparing to unpack .../018-libmpc3_1.3.1-1build2_amd64.deb ... 178s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 178s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 178s Preparing to unpack .../019-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package cpp-14. 178s Preparing to unpack .../020-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package cpp-x86-64-linux-gnu. 178s Preparing to unpack .../021-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 178s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 178s Selecting previously unselected package cpp. 178s Preparing to unpack .../022-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 178s Unpacking cpp (4:14.1.0-2ubuntu1) ... 178s Selecting previously unselected package libcc1-0:amd64. 178s Preparing to unpack .../023-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libgomp1:amd64. 178s Preparing to unpack .../024-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libitm1:amd64. 178s Preparing to unpack .../025-libitm1_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libasan8:amd64. 178s Preparing to unpack .../026-libasan8_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package liblsan0:amd64. 178s Preparing to unpack .../027-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libtsan2:amd64. 178s Preparing to unpack .../028-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 178s Selecting previously unselected package libubsan1:amd64. 178s Preparing to unpack .../029-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 178s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package libhwasan0:amd64. 179s Preparing to unpack .../030-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package libquadmath0:amd64. 179s Preparing to unpack .../031-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package libgcc-14-dev:amd64. 179s Preparing to unpack .../032-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 179s Preparing to unpack .../033-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package gcc-14. 179s Preparing to unpack .../034-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 179s Selecting previously unselected package gcc-x86-64-linux-gnu. 179s Preparing to unpack .../035-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 179s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 179s Selecting previously unselected package gcc. 179s Preparing to unpack .../036-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 179s Unpacking gcc (4:14.1.0-2ubuntu1) ... 179s Selecting previously unselected package libstdc++-14-dev:amd64. 179s Preparing to unpack .../037-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 179s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 180s Selecting previously unselected package g++-14-x86-64-linux-gnu. 180s Preparing to unpack .../038-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 180s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 180s Selecting previously unselected package g++-14. 180s Preparing to unpack .../039-g++-14_14.2.0-8ubuntu1_amd64.deb ... 180s Unpacking g++-14 (14.2.0-8ubuntu1) ... 180s Selecting previously unselected package g++-x86-64-linux-gnu. 180s Preparing to unpack .../040-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 180s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 180s Selecting previously unselected package g++. 180s Preparing to unpack .../041-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 180s Unpacking g++ (4:14.1.0-2ubuntu1) ... 180s Selecting previously unselected package build-essential. 180s Preparing to unpack .../042-build-essential_12.10ubuntu1_amd64.deb ... 180s Unpacking build-essential (12.10ubuntu1) ... 180s Selecting previously unselected package libblas3:amd64. 180s Preparing to unpack .../043-libblas3_3.12.0-3build2_amd64.deb ... 180s Unpacking libblas3:amd64 (3.12.0-3build2) ... 180s Selecting previously unselected package libgfortran5:amd64. 180s Preparing to unpack .../044-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 180s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 180s Selecting previously unselected package liblapack3:amd64. 180s Preparing to unpack .../045-liblapack3_3.12.0-3build2_amd64.deb ... 180s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 180s Selecting previously unselected package python3-numpy. 180s Preparing to unpack .../046-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 180s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 180s Selecting previously unselected package python3.12-tk. 180s Preparing to unpack .../047-python3.12-tk_3.12.7-3_amd64.deb ... 180s Unpacking python3.12-tk (3.12.7-3) ... 180s Selecting previously unselected package python3.13-tk. 180s Preparing to unpack .../048-python3.13-tk_3.13.0-2_amd64.deb ... 180s Unpacking python3.13-tk (3.13.0-2) ... 180s Selecting previously unselected package python3-tk:amd64. 180s Preparing to unpack .../049-python3-tk_3.12.7-1_amd64.deb ... 180s Unpacking python3-tk:amd64 (3.12.7-1) ... 180s Selecting previously unselected package python3-pil.imagetk:amd64. 180s Preparing to unpack .../050-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 180s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 180s Selecting previously unselected package libimagequant0:amd64. 181s Preparing to unpack .../051-libimagequant0_2.18.0-1build1_amd64.deb ... 181s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 181s Selecting previously unselected package libjpeg-turbo8:amd64. 181s Preparing to unpack .../052-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 182s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 182s Selecting previously unselected package libjpeg8:amd64. 182s Preparing to unpack .../053-libjpeg8_8c-2ubuntu11_amd64.deb ... 182s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 182s Selecting previously unselected package liblcms2-2:amd64. 182s Preparing to unpack .../054-liblcms2-2_2.16-2_amd64.deb ... 182s Unpacking liblcms2-2:amd64 (2.16-2) ... 182s Selecting previously unselected package libopenjp2-7:amd64. 182s Preparing to unpack .../055-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 182s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 182s Selecting previously unselected package libgraphite2-3:amd64. 182s Preparing to unpack .../056-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 182s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 182s Selecting previously unselected package libharfbuzz0b:amd64. 182s Preparing to unpack .../057-libharfbuzz0b_10.0.1-1_amd64.deb ... 182s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 182s Selecting previously unselected package libraqm0:amd64. 182s Preparing to unpack .../058-libraqm0_0.10.1-1build1_amd64.deb ... 182s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 182s Selecting previously unselected package libdeflate0:amd64. 182s Preparing to unpack .../059-libdeflate0_1.22-1_amd64.deb ... 182s Unpacking libdeflate0:amd64 (1.22-1) ... 182s Selecting previously unselected package libjbig0:amd64. 182s Preparing to unpack .../060-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 182s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 182s Selecting previously unselected package liblerc4:amd64. 182s Preparing to unpack .../061-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 182s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 182s Selecting previously unselected package libsharpyuv0:amd64. 182s Preparing to unpack .../062-libsharpyuv0_1.4.0-0.1_amd64.deb ... 182s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 182s Selecting previously unselected package libwebp7:amd64. 182s Preparing to unpack .../063-libwebp7_1.4.0-0.1_amd64.deb ... 182s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 182s Selecting previously unselected package libtiff6:amd64. 182s Preparing to unpack .../064-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 182s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 182s Selecting previously unselected package libwebpdemux2:amd64. 182s Preparing to unpack .../065-libwebpdemux2_1.4.0-0.1_amd64.deb ... 182s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 182s Selecting previously unselected package libwebpmux3:amd64. 182s Preparing to unpack .../066-libwebpmux3_1.4.0-0.1_amd64.deb ... 182s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 182s Selecting previously unselected package python3-pil:amd64. 182s Preparing to unpack .../067-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 182s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 182s Selecting previously unselected package libpixman-1-0:amd64. 182s Preparing to unpack .../068-libpixman-1-0_0.44.0-3_amd64.deb ... 182s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 182s Selecting previously unselected package libxcb-render0:amd64. 182s Preparing to unpack .../069-libxcb-render0_1.17.0-2_amd64.deb ... 182s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 182s Selecting previously unselected package libxcb-shm0:amd64. 182s Preparing to unpack .../070-libxcb-shm0_1.17.0-2_amd64.deb ... 182s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 182s Selecting previously unselected package libcairo2:amd64. 182s Preparing to unpack .../071-libcairo2_1.18.2-2_amd64.deb ... 182s Unpacking libcairo2:amd64 (1.18.2-2) ... 182s Selecting previously unselected package python3-cairo. 182s Preparing to unpack .../072-python3-cairo_1.26.1-2_amd64.deb ... 182s Unpacking python3-cairo (1.26.1-2) ... 182s Selecting previously unselected package python3-freetype. 182s Preparing to unpack .../073-python3-freetype_2.5.1-1_all.deb ... 182s Unpacking python3-freetype (2.5.1-1) ... 182s Selecting previously unselected package python3-rlpycairo. 182s Preparing to unpack .../074-python3-rlpycairo_0.3.0-3_all.deb ... 182s Unpacking python3-rlpycairo (0.3.0-3) ... 182s Selecting previously unselected package python3-reportlab. 182s Preparing to unpack .../075-python3-reportlab_4.2.5-1_all.deb ... 182s Unpacking python3-reportlab (4.2.5-1) ... 182s Selecting previously unselected package xml-core. 182s Preparing to unpack .../076-xml-core_0.19_all.deb ... 182s Unpacking xml-core (0.19) ... 182s Selecting previously unselected package w3c-sgml-lib. 182s Preparing to unpack .../077-w3c-sgml-lib_1.3-3_all.deb ... 182s Unpacking w3c-sgml-lib (1.3-3) ... 182s Selecting previously unselected package python3-biopython. 182s Preparing to unpack .../078-python3-biopython_1.84+dfsg-4_amd64.deb ... 182s Unpacking python3-biopython (1.84+dfsg-4) ... 182s Selecting previously unselected package libjs-jquery. 182s Preparing to unpack .../079-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 182s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 182s Selecting previously unselected package libjs-jquery-ui. 182s Preparing to unpack .../080-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 182s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 182s Selecting previously unselected package fonts-lyx. 182s Preparing to unpack .../081-fonts-lyx_2.4.2.1-1_all.deb ... 182s Unpacking fonts-lyx (2.4.2.1-1) ... 182s Selecting previously unselected package python-matplotlib-data. 182s Preparing to unpack .../082-python-matplotlib-data_3.8.3-3_all.deb ... 182s Unpacking python-matplotlib-data (3.8.3-3) ... 182s Selecting previously unselected package python3-six. 182s Preparing to unpack .../083-python3-six_1.16.0-7_all.deb ... 182s Unpacking python3-six (1.16.0-7) ... 182s Selecting previously unselected package python3-dateutil. 182s Preparing to unpack .../084-python3-dateutil_2.9.0-2_all.deb ... 182s Unpacking python3-dateutil (2.9.0-2) ... 182s Selecting previously unselected package python3-contourpy. 182s Preparing to unpack .../085-python3-contourpy_1.3.0-2_amd64.deb ... 182s Unpacking python3-contourpy (1.3.0-2) ... 182s Selecting previously unselected package python3-cycler. 182s Preparing to unpack .../086-python3-cycler_0.12.1-1_all.deb ... 182s Unpacking python3-cycler (0.12.1-1) ... 182s Selecting previously unselected package python3-brotli. 182s Preparing to unpack .../087-python3-brotli_1.1.0-2build2_amd64.deb ... 182s Unpacking python3-brotli (1.1.0-2build2) ... 182s Selecting previously unselected package python3-decorator. 182s Preparing to unpack .../088-python3-decorator_5.1.1-5_all.deb ... 182s Unpacking python3-decorator (5.1.1-5) ... 182s Selecting previously unselected package liblbfgsb0:amd64. 182s Preparing to unpack .../089-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 182s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 182s Selecting previously unselected package python3-scipy. 182s Preparing to unpack .../090-python3-scipy_1.13.1-5_amd64.deb ... 182s Unpacking python3-scipy (1.13.1-5) ... 183s Selecting previously unselected package python3-ufolib2. 183s Preparing to unpack .../091-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 183s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 183s Selecting previously unselected package python3-mpmath. 183s Preparing to unpack .../092-python3-mpmath_1.3.0-1_all.deb ... 183s Unpacking python3-mpmath (1.3.0-1) ... 183s Selecting previously unselected package python3-sympy. 183s Preparing to unpack .../093-python3-sympy_1.13.3-1_all.deb ... 183s Unpacking python3-sympy (1.13.3-1) ... 183s Selecting previously unselected package python3-tz. 183s Preparing to unpack .../094-python3-tz_2024.1-2_all.deb ... 183s Unpacking python3-tz (2024.1-2) ... 183s Selecting previously unselected package python3-appdirs. 183s Preparing to unpack .../095-python3-appdirs_1.4.4-4_all.deb ... 183s Unpacking python3-appdirs (1.4.4-4) ... 183s Selecting previously unselected package python3-fs. 183s Preparing to unpack .../096-python3-fs_2.4.16-4_all.deb ... 183s Unpacking python3-fs (2.4.16-4) ... 183s Selecting previously unselected package libxslt1.1:amd64. 183s Preparing to unpack .../097-libxslt1.1_1.1.39-0exp1ubuntu1_amd64.deb ... 183s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 184s Selecting previously unselected package python3-lxml:amd64. 184s Preparing to unpack .../098-python3-lxml_5.3.0-1_amd64.deb ... 184s Unpacking python3-lxml:amd64 (5.3.0-1) ... 184s Selecting previously unselected package python3-lz4. 184s Preparing to unpack .../099-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 184s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 184s Selecting previously unselected package python3-unicodedata2. 184s Preparing to unpack .../100-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 184s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 184s Selecting previously unselected package unicode-data. 184s Preparing to unpack .../101-unicode-data_15.1.0-1_all.deb ... 184s Unpacking unicode-data (15.1.0-1) ... 184s Selecting previously unselected package python3-fonttools. 184s Preparing to unpack .../102-python3-fonttools_4.46.0-1build2_amd64.deb ... 184s Unpacking python3-fonttools (4.46.0-1build2) ... 184s Selecting previously unselected package python3-kiwisolver. 184s Preparing to unpack .../103-python3-kiwisolver_1.4.7-2_amd64.deb ... 184s Unpacking python3-kiwisolver (1.4.7-2) ... 184s Selecting previously unselected package python3-packaging. 184s Preparing to unpack .../104-python3-packaging_24.1-1_all.deb ... 184s Unpacking python3-packaging (24.1-1) ... 184s Selecting previously unselected package libqhull-r8.0:amd64. 184s Preparing to unpack .../105-libqhull-r8.0_2020.2-6build1_amd64.deb ... 184s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 184s Selecting previously unselected package python3-matplotlib. 184s Preparing to unpack .../106-python3-matplotlib_3.8.3-3_amd64.deb ... 184s Unpacking python3-matplotlib (3.8.3-3) ... 184s Selecting previously unselected package python3-pandas-lib:amd64. 184s Preparing to unpack .../107-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ... 184s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 184s Selecting previously unselected package python3-pandas. 184s Preparing to unpack .../108-python3-pandas_2.2.3+dfsg-5_all.deb ... 184s Unpacking python3-pandas (2.2.3+dfsg-5) ... 185s Selecting previously unselected package python3-joblib. 185s Preparing to unpack .../109-python3-joblib_1.3.2-5_all.deb ... 185s Unpacking python3-joblib (1.3.2-5) ... 185s Selecting previously unselected package python3-networkx. 185s Preparing to unpack .../110-python3-networkx_3.2.1-4ubuntu1_all.deb ... 185s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 185s Selecting previously unselected package python3-pomegranate. 185s Preparing to unpack .../111-python3-pomegranate_0.14.8-6_amd64.deb ... 185s Unpacking python3-pomegranate (0.14.8-6) ... 186s Selecting previously unselected package python3-importlib-metadata. 186s Preparing to unpack .../112-python3-importlib-metadata_8.5.0-1_all.deb ... 186s Unpacking python3-importlib-metadata (8.5.0-1) ... 186s Selecting previously unselected package python3-pyfaidx. 186s Preparing to unpack .../113-python3-pyfaidx_0.8.1.3-1_all.deb ... 186s Unpacking python3-pyfaidx (0.8.1.3-1) ... 186s Selecting previously unselected package libhtscodecs2:amd64. 186s Preparing to unpack .../114-libhtscodecs2_1.6.1-1_amd64.deb ... 186s Unpacking libhtscodecs2:amd64 (1.6.1-1) ... 186s Selecting previously unselected package libhts3t64:amd64. 186s Preparing to unpack .../115-libhts3t64_1.20+ds-1_amd64.deb ... 186s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 186s Selecting previously unselected package python3-pysam. 186s Preparing to unpack .../116-python3-pysam_0.22.1+ds-2_amd64.deb ... 186s Unpacking python3-pysam (0.22.1+ds-2) ... 186s Selecting previously unselected package python3-threadpoolctl. 186s Preparing to unpack .../117-python3-threadpoolctl_3.1.0-1_all.deb ... 186s Unpacking python3-threadpoolctl (3.1.0-1) ... 186s Selecting previously unselected package python3-sklearn-lib:amd64. 186s Preparing to unpack .../118-python3-sklearn-lib_1.4.2+dfsg-6_amd64.deb ... 186s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 186s Selecting previously unselected package python3-sklearn. 186s Preparing to unpack .../119-python3-sklearn_1.4.2+dfsg-6_all.deb ... 186s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 186s Selecting previously unselected package zip. 186s Preparing to unpack .../120-zip_3.0-14ubuntu1_amd64.deb ... 186s Unpacking zip (3.0-14ubuntu1) ... 186s Selecting previously unselected package unzip. 186s Preparing to unpack .../121-unzip_6.0-28ubuntu6_amd64.deb ... 186s Unpacking unzip (6.0-28ubuntu6) ... 186s Selecting previously unselected package libpaper1:amd64. 186s Preparing to unpack .../122-libpaper1_1.1.29build1_amd64.deb ... 186s Unpacking libpaper1:amd64 (1.1.29build1) ... 186s Selecting previously unselected package libpaper-utils. 186s Preparing to unpack .../123-libpaper-utils_1.1.29build1_amd64.deb ... 186s Unpacking libpaper-utils (1.1.29build1) ... 186s Selecting previously unselected package xdg-utils. 186s Preparing to unpack .../124-xdg-utils_1.2.1-0ubuntu1_all.deb ... 186s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 187s Selecting previously unselected package fontconfig. 187s Preparing to unpack .../125-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ... 187s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 187s Selecting previously unselected package libthai-data. 187s Preparing to unpack .../126-libthai-data_0.1.29-2build1_all.deb ... 187s Unpacking libthai-data (0.1.29-2build1) ... 187s Selecting previously unselected package libdatrie1:amd64. 187s Preparing to unpack .../127-libdatrie1_0.2.13-3build1_amd64.deb ... 187s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 187s Selecting previously unselected package libthai0:amd64. 187s Preparing to unpack .../128-libthai0_0.1.29-2build1_amd64.deb ... 187s Unpacking libthai0:amd64 (0.1.29-2build1) ... 187s Selecting previously unselected package libpango-1.0-0:amd64. 187s Preparing to unpack .../129-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... 187s Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... 187s Selecting previously unselected package libpangoft2-1.0-0:amd64. 187s Preparing to unpack .../130-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... 187s Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 187s Selecting previously unselected package libpangocairo-1.0-0:amd64. 187s Preparing to unpack .../131-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... 187s Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 187s Selecting previously unselected package libice6:amd64. 187s Preparing to unpack .../132-libice6_2%3a1.1.1-1_amd64.deb ... 187s Unpacking libice6:amd64 (2:1.1.1-1) ... 187s Selecting previously unselected package libsm6:amd64. 187s Preparing to unpack .../133-libsm6_2%3a1.2.4-1_amd64.deb ... 187s Unpacking libsm6:amd64 (2:1.2.4-1) ... 187s Selecting previously unselected package libxt6t64:amd64. 187s Preparing to unpack .../134-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 187s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 187s Selecting previously unselected package r-base-core. 187s Preparing to unpack .../135-r-base-core_4.4.2-1_amd64.deb ... 187s Unpacking r-base-core (4.4.2-1) ... 187s Selecting previously unselected package r-bioc-biocgenerics. 187s Preparing to unpack .../136-r-bioc-biocgenerics_0.50.0-2_all.deb ... 187s Unpacking r-bioc-biocgenerics (0.50.0-2) ... 187s Selecting previously unselected package r-bioc-dnacopy. 187s Preparing to unpack .../137-r-bioc-dnacopy_1.78.0-1_amd64.deb ... 187s Unpacking r-bioc-dnacopy (1.78.0-1) ... 187s Selecting previously unselected package cnvkit. 187s Preparing to unpack .../138-cnvkit_0.9.10-2_all.deb ... 187s Unpacking cnvkit (0.9.10-2) ... 188s Selecting previously unselected package libpoppler140:amd64. 188s Preparing to unpack .../139-libpoppler140_24.08.0-1_amd64.deb ... 188s Unpacking libpoppler140:amd64 (24.08.0-1) ... 188s Selecting previously unselected package poppler-utils. 188s Preparing to unpack .../140-poppler-utils_24.08.0-1_amd64.deb ... 188s Unpacking poppler-utils (24.08.0-1) ... 188s Setting up libhtscodecs2:amd64 (1.6.1-1) ... 188s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 188s Setting up liblcms2-2:amd64 (2.16-2) ... 188s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 188s Setting up libsharpyuv0:amd64 (1.4.0-0.1) ... 188s Setting up libpaper1:amd64 (1.1.29build1) ... 188s 188s Creating config file /etc/papersize with new version 188s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 188s Setting up python3-importlib-metadata (8.5.0-1) ... 188s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 188s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 188s Setting up python3-joblib (1.3.2-5) ... 189s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 189s Setting up libxcb-render0:amd64 (1.17.0-2) ... 189s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 189s Setting up fonts-lyx (2.4.2.1-1) ... 189s Setting up unzip (6.0-28ubuntu6) ... 189s Setting up python3-threadpoolctl (3.1.0-1) ... 189s Setting up x11-common (1:7.7+23ubuntu3) ... 189s Setting up libdeflate0:amd64 (1.22-1) ... 189s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 189s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 189s Setting up libpaper-utils (1.1.29build1) ... 189s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 189s Setting up python3-freetype (2.5.1-1) ... 189s Setting up python3-networkx (3.2.1-4ubuntu1) ... 191s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 191s Setting up python3-tz (2024.1-2) ... 191s Setting up unicode-data (15.1.0-1) ... 191s Setting up python3-six (1.16.0-7) ... 191s Setting up python3-decorator (5.1.1-5) ... 191s Setting up zip (3.0-14ubuntu1) ... 191s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 191s Setting up libblas3:amd64 (3.12.0-3build2) ... 191s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 191s Setting up python3-packaging (24.1-1) ... 191s Setting up python3-brotli (1.1.0-2build2) ... 191s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 191s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 191s Setting up python3-cycler (0.12.1-1) ... 191s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 191s Setting up fonts-dejavu-mono (2.37-8) ... 191s Setting up python3-kiwisolver (1.4.7-2) ... 192s Setting up libmpc3:amd64 (1.3.1-1build2) ... 192s Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... 192s Setting up fonts-dejavu-core (2.37-8) ... 192s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 192s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libwebp7:amd64 (1.4.0-0.1) ... 192s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu1) ... 192s Setting up libhts3t64:amd64 (1.20+ds-1) ... 192s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 192s Setting up libharfbuzz0b:amd64 (10.0.1-1) ... 192s Setting up libthai-data (0.1.29-2build1) ... 192s Setting up python3-dateutil (2.9.0-2) ... 192s Setting up sgml-base (1.31) ... 192s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 192s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 192s Setting up python3-mpmath (1.3.0-1) ... 192s Setting up libisl23:amd64 (0.27-1) ... 192s Setting up python-matplotlib-data (3.8.3-3) ... 192s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 192s Setting up python3-appdirs (1.4.4-4) ... 192s Setting up xdg-utils (1.2.1-0ubuntu1) ... 192s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 192s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 192s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 192s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 192s Setting up python3-pyfaidx (0.8.1.3-1) ... 193s Setting up python3-sympy (1.13.3-1) ... 199s Setting up libice6:amd64 (2:1.1.1-1) ... 199s Setting up liblapack3:amd64 (3.12.0-3build2) ... 199s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 199s Setting up python3-pysam (0.22.1+ds-2) ... 199s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 199s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 199s Setting up xfonts-utils (1:7.7+7) ... 199s Setting up python3-fs (2.4.16-4) ... 199s Setting up libthai0:amd64 (0.1.29-2build1) ... 199s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 199s Setting up libraqm0:amd64 (0.10.1-1build1) ... 199s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 199s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 201s Setting up cpp-14 (14.2.0-8ubuntu1) ... 201s Setting up python3-lxml:amd64 (5.3.0-1) ... 201s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 201s Setting up xml-core (0.19) ... 202s Setting up python3-contourpy (1.3.0-2) ... 202s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 202s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 202s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 202s Setting up libsm6:amd64 (2:1.2.4-1) ... 202s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 202s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 202s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 204s Regenerating fonts cache... done. 204s Setting up libxft2:amd64 (2.3.6-1build1) ... 204s Setting up python3-scipy (1.13.1-5) ... 207s Setting up python3-pomegranate (0.14.8-6) ... 208s Setting up libtk8.6:amd64 (8.6.15-1) ... 208s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 208s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... 208s Setting up python3.12-tk (3.12.7-3) ... 208s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 208s Setting up fonts-urw-base35 (20200910-8) ... 208s Setting up libcairo2:amd64 (1.18.2-2) ... 208s Setting up python3.13-tk (3.13.0-2) ... 208s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 208s Setting up python3-pandas (2.2.3+dfsg-5) ... 214s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 214s Setting up python3-sklearn (1.4.2+dfsg-6) ... 216s Setting up cpp (4:14.1.0-2ubuntu1) ... 216s Setting up libpoppler140:amd64 (24.08.0-1) ... 216s Setting up poppler-utils (24.08.0-1) ... 216s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 216s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 216s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 216s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 216s Setting up python3-cairo (1.26.1-2) ... 216s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 216s Setting up blt (2.5.3+dfsg-7build1) ... 216s Setting up python3-tk:amd64 (3.12.7-1) ... 216s Setting up gcc-14 (14.2.0-8ubuntu1) ... 216s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 216s Setting up python3-rlpycairo (0.3.0-3) ... 216s Setting up r-base-core (4.4.2-1) ... 216s 216s Creating config file /etc/R/Renviron with new version 216s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 216s Setting up python3-reportlab (4.2.5-1) ... 217s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 217s Setting up g++-14 (14.2.0-8ubuntu1) ... 217s Setting up r-bioc-biocgenerics (0.50.0-2) ... 217s Setting up gcc (4:14.1.0-2ubuntu1) ... 217s Setting up g++ (4:14.1.0-2ubuntu1) ... 217s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 217s Setting up r-bioc-dnacopy (1.78.0-1) ... 217s Setting up build-essential (12.10ubuntu1) ... 217s Setting up python3-fonttools (4.46.0-1build2) ... 218s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 218s Setting up python3-matplotlib (3.8.3-3) ... 219s Processing triggers for libc-bin (2.40-1ubuntu3) ... 219s Processing triggers for man-db (2.12.1-3) ... 221s Processing triggers for install-info (7.1.1-1) ... 221s Processing triggers for sgml-base (1.31) ... 221s Setting up w3c-sgml-lib (1.3-3) ... 249s Setting up python3-biopython (1.84+dfsg-4) ... 250s Setting up cnvkit (0.9.10-2) ... 251s Reading package lists... 251s Building dependency tree... 251s Reading state information... 252s Starting pkgProblemResolver with broken count: 0 252s Starting 2 pkgProblemResolver with broken count: 0 252s Done 252s The following NEW packages will be installed: 252s autopkgtest-satdep 252s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 252s Need to get 0 B/696 B of archives. 252s After this operation, 0 B of additional disk space will be used. 252s Get:1 /tmp/autopkgtest.lQrRjI/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 253s Selecting previously unselected package autopkgtest-satdep. 253s (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 ... 94066 files and directories currently installed.) 253s Preparing to unpack .../2-autopkgtest-satdep.deb ... 253s Unpacking autopkgtest-satdep (0) ... 253s Setting up autopkgtest-satdep (0) ... 271s (Reading database ... 94066 files and directories currently installed.) 271s Removing autopkgtest-satdep (0) ... 279s autopkgtest [12:28:52]: test run-unit-test: [----------------------- 285s cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ 287s Created directory build/ 287s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 287s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 287s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 287s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 287s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 287s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 287s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 287s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 287s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 288s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 289s Number of target and antitarget files: 3, 3 289s No FASTA reference genome provided; skipping GC, RM calculations 289s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 289s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 289s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 289s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 289s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 289s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 289s Loading build/p2-20_5.targetcoverage.cnn 290s Correcting for GC bias... 290s Correcting for density bias... 290s Loading build/p2-5_5.targetcoverage.cnn 290s Correcting for GC bias... 290s Correcting for density bias... 290s Loading build/p2-9_5.targetcoverage.cnn 290s Correcting for GC bias... 290s Correcting for density bias... 290s Loading build/p2-20_5.antitargetcoverage.cnn 290s Correcting for GC bias... 290s Loading build/p2-5_5.antitargetcoverage.cnn 290s Correcting for GC bias... 290s Loading build/p2-9_5.antitargetcoverage.cnn 290s Correcting for GC bias... 290s Calculating average bin coverages 297s Calculating bin spreads 300s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 300s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 300s " chr1:2435319-2436685 log2=-0.709 spread=0.503 300s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 300s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 300s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 300s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 300s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 300s " chr1:120611883-120612051 log2=0.070 spread=0.050 300s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 300s " chr1:156842391-156842479 log2=-0.398 spread=0.290 300s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 300s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 300s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 300s " chr1:183481886-183481951 log2=-0.040 spread=0.119 300s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 300s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 300s " chr1:243800859-243801066 log2=0.023 spread=0.063 300s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 300s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 300s " chr2:25536716-25536891 log2=0.702 spread=0.033 300s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 300s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 300s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 300s REL chr2:61108881-61109061 log2=1.026 spread=0.559 300s " chr2:61128072-61128256 log2=0.115 spread=0.173 300s " chr2:61145275-61145462 log2=0.014 spread=0.099 300s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 300s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 300s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 300s " chr2:128095237-128095425 log2=0.215 spread=0.212 300s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 300s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 300s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 300s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 300s " chr3:97160189-97160367 log2=-0.050 spread=0.191 300s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 300s " chr3:142286854-142287031 log2=-0.076 spread=0.116 300s GAK chr4:896278-896357 log2=-1.505 spread=1.261 300s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 300s " chr4:1803044-1803507 log2=-0.073 spread=0.117 300s " chr4:1808792-1809022 log2=0.252 spread=0.108 300s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 300s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 300s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 300s " chr4:178514600-178514725 log2=-0.098 spread=0.096 300s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 300s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 300s " chr5:1295312-1295381 log2=-0.690 spread=0.462 300s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 300s " chr5:25519857-25520034 log2=-0.015 spread=0.095 300s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 300s " chr5:38962338-38962525 log2=0.005 spread=0.019 300s " chr5:38966685-38966862 log2=0.006 spread=0.165 300s " chr5:38978620-38978763 log2=0.040 spread=0.030 300s " chr5:39074133-39074327 log2=-0.158 spread=0.139 300s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 300s " chr5:51030131-51030313 log2=-0.034 spread=0.192 300s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 300s " chr5:56168412-56168590 log2=0.479 spread=0.038 300s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 300s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 300s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 300s " chr5:86637023-86637168 log2=0.054 spread=0.111 300s " chr5:86642414-86642592 log2=0.254 spread=0.162 300s " chr5:86648912-86649096 log2=0.092 spread=0.062 300s " chr5:86670598-86670778 log2=0.222 spread=0.198 300s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 300s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 300s APC chr5:112101965-112102138 log2=0.104 spread=0.217 300s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 300s " chr5:170837567-170837631 log2=0.085 spread=0.349 300s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 300s " chr5:180046203-180046404 log2=-1.531 spread=0.722 300s " chr5:180076418-180076603 log2=-2.224 spread=1.416 300s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 300s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 300s " chr6:31939599-31940313 log2=-19.582 spread=0.181 300s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 300s " chr6:31946632-31946824 log2=-20.052 spread=0.088 300s " chr6:31947142-31947366 log2=-20.114 spread=0.066 300s " chr6:31948176-31948360 log2=-19.982 spread=0.149 300s " chr6:31948382-31948612 log2=-19.757 spread=0.165 300s " chr6:31948730-31949253 log2=-20.048 spread=0.014 300s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 300s " chr6:32164046-32164227 log2=-19.755 spread=0.189 300s " chr6:32164652-32164888 log2=-19.984 spread=0.154 300s " chr6:32165021-32165403 log2=-19.625 spread=0.196 300s " chr6:32166163-32166545 log2=-20.043 spread=0.072 300s " chr6:32166648-32166962 log2=-3.514 spread=5.742 300s " chr6:32168554-32168821 log2=-19.601 spread=0.197 300s " chr6:32168844-32169306 log2=-19.683 spread=0.166 300s " chr6:32169801-32170391 log2=-19.405 spread=0.205 300s " chr6:32171492-32171691 log2=-20.095 spread=0.101 300s " chr6:32171861-32172198 log2=-3.141 spread=7.288 300s " chr6:32178478-32178749 log2=-19.927 spread=0.164 300s " chr6:32180197-32180441 log2=-10.902 spread=9.532 300s " chr6:32180544-32180722 log2=-19.675 spread=0.186 300s " chr6:32180857-32181062 log2=-19.562 spread=0.227 300s " chr6:32181411-32181646 log2=-19.966 spread=0.171 300s " chr6:32181832-32182066 log2=-19.961 spread=0.172 300s " chr6:32182948-32183194 log2=-19.935 spread=0.168 300s " chr6:32184667-32185079 log2=-19.923 spread=0.165 300s " chr6:32185720-32185919 log2=-19.707 spread=0.197 300s " chr6:32187317-32187601 log2=-19.765 spread=0.173 300s " chr6:32187871-32188094 log2=-19.660 spread=0.188 300s " chr6:32188127-32188451 log2=-19.622 spread=0.169 300s " chr6:32188481-32188693 log2=-19.902 spread=0.132 300s " chr6:32188704-32189133 log2=-19.501 spread=0.193 300s " chr6:32190258-32190616 log2=-19.570 spread=0.209 300s " chr6:32190724-32190908 log2=-19.540 spread=0.232 300s " chr6:32191570-32191668 log2=-19.773 spread=0.178 300s " chr6:32191676-32191753 log2=-19.374 spread=0.201 300s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 300s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 300s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 300s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 300s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 300s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 300s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 300s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 300s " chr6:128316545-128316699 log2=-0.070 spread=0.050 300s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 300s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 300s " chr6:157099442-157099991 log2=-0.846 spread=0.504 300s " chr6:157100042-157100634 log2=-1.570 spread=0.825 300s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 300s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 300s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 300s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 300s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 300s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 300s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 300s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 300s " chr7:98491365-98491541 log2=0.209 spread=0.153 300s " chr7:98493314-98493496 log2=0.389 spread=0.207 300s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 300s " chr7:128829048-128829358 log2=-0.474 spread=0.315 300s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 300s " chr7:140484736-140484912 log2=0.081 spread=0.150 300s " chr7:140487956-140488430 log2=-0.089 spread=0.142 300s " chr7:140493336-140493442 log2=-0.340 spread=0.283 300s " chr7:140624315-140624540 log2=-0.497 spread=0.342 300s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 300s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 300s " chr8:30941153-30941335 log2=0.079 spread=0.294 300s " chr8:30942625-30942802 log2=0.044 spread=0.247 300s " chr8:30947918-30948092 log2=0.151 spread=0.124 300s " chr8:31000128-31000252 log2=-0.099 spread=0.098 300s " chr8:31001006-31001182 log2=-0.002 spread=0.062 300s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 300s " chr8:37698557-37699898 log2=-0.612 spread=0.029 300s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 300s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 300s " chr8:48845528-48845758 log2=0.056 spread=0.196 300s " chr8:48866846-48867043 log2=-0.067 spread=0.097 300s " chr8:48868369-48868526 log2=-0.239 spread=0.174 300s " chr8:48872485-48872722 log2=-0.636 spread=0.464 300s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 300s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 300s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 300s " chr9:2101491-2101640 log2=0.244 spread=0.104 300s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 300s " chr9:5067014-5067883 log2=0.146 spread=0.089 300s " chr9:5068184-5070306 log2=0.133 spread=0.092 300s " chr9:5076944-5077152 log2=0.046 spread=0.137 300s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 300s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 300s " chr9:21986759-21986899 log2=0.058 spread=0.175 300s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 300s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 300s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 300s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 300s " chr9:87425375-87425452 log2=0.494 spread=0.066 300s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 300s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 300s " chr9:139250747-139251032 log2=-0.223 spread=0.273 300s " chr9:139252418-139252703 log2=-0.512 spread=0.264 300s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 300s " chr9:139417262-139417677 log2=-0.173 spread=0.191 300s " chr9:139440110-139440287 log2=-1.257 spread=0.500 300s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 300s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 300s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 300s " chr10:43600360-43600677 log2=-0.341 spread=0.222 300s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 300s " chr10:89685254-89685374 log2=0.244 spread=0.259 300s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 300s " chr10:93579008-93579121 log2=0.166 spread=0.220 300s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 300s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 300s " chr10:112679716-112679934 log2=-0.008 spread=0.028 300s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 300s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 300s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 300s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 300s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 300s " chr11:94170270-94170454 log2=0.095 spread=0.285 300s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 300s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 300s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 300s " chr11:108164020-108164234 log2=-0.056 spread=0.040 300s " chr11:108217986-108218135 log2=0.359 spread=0.277 300s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 300s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 300s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 300s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 300s " chr12:25391004-25391186 log2=0.368 spread=0.128 300s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 300s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 300s " chr12:51206782-51207287 log2=-0.012 spread=0.101 300s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 300s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 300s " chr13:26970356-26970536 log2=0.137 spread=0.121 300s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 300s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 300s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 300s " chr13:32903506-32903689 log2=0.019 spread=0.232 300s " chr13:32918645-32918823 log2=0.158 spread=0.114 300s " chr13:32920899-32921077 log2=0.014 spread=0.247 300s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 300s " chr13:48919164-48919369 log2=0.025 spread=0.094 300s " chr13:48921877-48922044 log2=0.106 spread=0.147 300s " chr13:48923026-48923204 log2=0.360 spread=0.016 300s " chr13:48938965-48939147 log2=0.084 spread=0.356 300s " chr13:48941578-48941767 log2=0.238 spread=0.212 300s " chr13:48947486-48947665 log2=0.025 spread=0.126 300s " chr13:48954166-48954251 log2=0.061 spread=0.273 300s " chr13:49037815-49038005 log2=0.063 spread=0.062 300s " chr13:49047410-49047589 log2=0.053 spread=0.170 300s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 300s " chr13:85527771-85527948 log2=0.007 spread=0.222 300s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 300s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 300s " chr13:110438332-110438432 log2=-3.643 spread=2.325 300s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 300s " chr14:20291466-20291612 log2=0.697 spread=0.248 300s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 300s " chr14:36989195-36989373 log2=0.023 spread=0.162 300s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 300s " chr14:50619741-50619923 log2=0.003 spread=0.272 300s " chr14:50697856-50698044 log2=0.277 spread=0.334 300s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 300s " chr14:71275790-71275923 log2=-2.815 spread=1.938 300s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 300s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 300s " chr15:38544477-38545455 log2=-0.348 spread=0.179 300s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 300s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 300s " chr15:41803968-41804185 log2=-2.202 spread=0.188 300s " chr15:41804261-41804494 log2=-0.402 spread=0.392 300s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 300s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 300s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 300s " chr16:2611404-2611585 log2=-5.171 spread=1.963 300s " chr16:2611721-2611943 log2=-11.810 spread=9.172 300s " chr16:2615504-2615725 log2=-20.113 spread=0.007 300s " chr16:2616307-2616486 log2=-20.054 spread=0.072 300s " chr16:2631267-2631414 log2=-20.009 spread=0.061 300s " chr16:2631583-2631734 log2=-20.089 spread=0.090 300s " chr16:2633363-2633616 log2=-20.101 spread=0.089 300s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 300s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 300s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 300s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 300s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 300s " chr16:50826460-50826650 log2=0.239 spread=0.204 300s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 300s " chr16:60005694-60005857 log2=-0.366 spread=0.298 300s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 300s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 300s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 300s " chr17:12011053-12011253 log2=0.028 spread=0.232 300s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 300s " chr17:29496854-29497046 log2=0.226 spread=0.193 300s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 300s " chr17:30519172-30519355 log2=0.163 spread=0.289 300s " chr17:30525911-30526093 log2=-0.157 spread=0.046 300s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 300s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 300s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 300s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 300s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 300s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 300s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 300s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 300s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 300s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 300s " chr19:2210351-2210545 log2=-0.860 spread=0.261 300s " chr19:2226130-2227152 log2=-0.113 spread=0.120 300s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 300s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 300s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 300s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 300s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 300s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 300s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 300s " chr19:15311544-15311749 log2=-1.887 spread=1.202 300s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 300s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 300s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 300s " chr19:33792774-33793010 log2=-1.781 spread=0.127 300s " chr19:33793014-33793356 log2=-0.541 spread=0.385 300s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 300s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 300s " chr19:45873698-45873881 log2=-0.522 spread=0.327 300s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 300s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 300s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 300s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 300s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 300s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 300s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 300s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 300s " chr21:36265140-36265318 log2=0.042 spread=0.039 300s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 300s " chr22:29115325-29115465 log2=0.055 spread=0.390 300s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 300s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 300s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 300s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 300s " chrX:1317372-1317594 log2=-21.121 spread=0.049 300s " chrX:1321225-1321435 log2=-20.851 spread=0.196 300s " chrX:1325274-1325530 log2=-21.121 spread=0.011 300s " chrX:1327651-1327830 log2=-21.000 spread=0.029 300s " chrX:1331391-1331576 log2=-21.018 spread=0.052 300s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 300s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 300s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 300s " chrX:123185143-123185290 log2=-1.018 spread=0.062 300s " chrX:123202378-123202544 log2=-0.959 spread=0.103 300s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 300s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 300s " chrY:9008607-9008759 log2=-1.012 spread=0.097 300s " chrY:13131970-13132039 log2=-1.004 spread=0.074 300s " chrY:19506485-19506650 log2=-1.018 spread=0.034 300s " chrY:21033918-21034071 log2=-1.013 spread=0.057 300s " chrY:28463435-28463622 log2=-0.952 spread=0.039 300s " chrY:28514033-28514208 log2=-0.992 spread=0.026 300s Antitargets: 108 (0.8597%) bins failed filters 300s Wrote build/reference-picard.cnn with 19209 regions 300s cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr 301s Processing target: p2-5_5 301s Keeping 6308 of 6646 bins 301s Correcting for GC bias... 301s Correcting for density bias... 301s Processing antitarget: p2-5_5 301s Keeping 12455 of 12563 bins 301s Correcting for GC bias... 301s WARNING: Skipping correction for RepeatMasker bias 301s Targets are 1.18 x more variable than antitargets 301s Wrote build/p2-5_5.cnr with 18763 regions 302s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 303s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 303s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 303s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 305s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 305s cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr 307s Processing target: p2-9_2 307s Keeping 6308 of 6646 bins 307s Correcting for GC bias... 307s Correcting for density bias... 307s Processing antitarget: p2-9_2 307s Keeping 12455 of 12563 bins 307s Correcting for GC bias... 307s WARNING: Skipping correction for RepeatMasker bias 307s Targets are 1.72 x more variable than antitargets 308s Wrote build/p2-9_2.cnr with 18763 regions 308s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 309s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 309s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 310s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 311s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 311s cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr 313s Processing target: p2-20_1 313s Keeping 6308 of 6646 bins 313s Correcting for GC bias... 313s Correcting for density bias... 313s Processing antitarget: p2-20_1 313s Keeping 12455 of 12563 bins 313s Correcting for GC bias... 313s WARNING: Skipping correction for RepeatMasker bias 313s Targets are 1.12 x more variable than antitargets 314s Wrote build/p2-20_1.cnr with 18763 regions 314s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 315s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 315s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 316s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 317s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 318s cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr 319s Processing target: p2-20_2 319s Keeping 6308 of 6646 bins 319s Correcting for GC bias... 319s Correcting for density bias... 319s Processing antitarget: p2-20_2 320s Keeping 12455 of 12563 bins 320s Correcting for GC bias... 320s WARNING: Skipping correction for RepeatMasker bias 320s Targets are 1.10 x more variable than antitargets 320s Wrote build/p2-20_2.cnr with 18763 regions 320s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 322s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 322s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 322s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 323s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 324s cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr 325s Processing target: p2-20_3 325s Keeping 6308 of 6646 bins 325s Correcting for GC bias... 325s Correcting for density bias... 326s Processing antitarget: p2-20_3 326s Keeping 12455 of 12563 bins 326s Correcting for GC bias... 326s WARNING: Skipping correction for RepeatMasker bias 326s Antitargets are 1.09 x more variable than targets 326s Wrote build/p2-20_3.cnr with 18763 regions 326s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 328s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 328s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 328s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 331s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 331s cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr 332s Processing target: p2-20_4 332s Keeping 6308 of 6646 bins 332s Correcting for GC bias... 332s Correcting for density bias... 332s Processing antitarget: p2-20_4 332s Keeping 12455 of 12563 bins 332s Correcting for GC bias... 332s WARNING: Skipping correction for RepeatMasker bias 332s Targets are 1.43 x more variable than antitargets 332s Wrote build/p2-20_4.cnr with 18763 regions 332s cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr 334s Processing target: p2-20_5 334s Keeping 6308 of 6646 bins 334s Correcting for GC bias... 334s Correcting for density bias... 334s Processing antitarget: p2-20_5 334s Keeping 12455 of 12563 bins 334s Correcting for GC bias... 334s WARNING: Skipping correction for RepeatMasker bias 335s Targets are 2.50 x more variable than antitargets 335s Wrote build/p2-20_5.cnr with 18763 regions 335s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 336s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 343s Dropped 8 / 49 bins on chromosome chrY 343s Wrote build/p2-5_5.cns with 71 regions 344s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 345s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 347s Dropped 1 / 949 bins on chromosome chr6 352s Dropped 27 / 49 bins on chromosome chrY 352s Wrote build/p2-9_2.cns with 103 regions 353s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 354s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 361s Dropped 6 / 49 bins on chromosome chrY 362s Wrote build/p2-20_1.cns with 121 regions 362s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 363s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 371s Dropped 7 / 49 bins on chromosome chrY 371s Wrote build/p2-20_2.cns with 117 regions 371s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 373s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 379s Dropped 11 / 49 bins on chromosome chrY 379s Wrote build/p2-20_3.cns with 64 regions 380s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 381s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 389s Dropped 8 / 49 bins on chromosome chrY 389s Wrote build/p2-20_4.cns with 143 regions 389s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 391s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 397s Smoothing overshot at 1 / 123 indices: (-0.30060035404086805, 0.32508880185194927) vs. original (-0.363302, 0.311218) 398s Dropped 6 / 49 bins on chromosome chrY 398s Wrote build/p2-20_5.cns with 120 regions 399s cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf 402s Wrote p2-5_5-scatter.pdf 402s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf 404s Smoothing overshot at 3 / 97 indices: (-19.900105868621722, -3.309906922372052) vs. original (-19.294, -0.16431) 405s Wrote p2-9_2-scatter.pdf 405s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 406s Showing 1480 probes and 0 selected genes in region chr1 407s Wrote p2-9_2-chr1-scatter.pdf 407s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 409s Showing 201 probes and 0 selected genes in region chr21 409s Wrote p2-9_2-chr21-scatter.pdf 409s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf 410s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 411s Wrote p2-9_2-chr9p-scatter.pdf 411s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf 412s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 413s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 413s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf 414s Detected file format: bed 414s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 414s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 415s which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf 415s /usr/bin/pdfunite 415s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 416s Treating sample p2-5_5 as female 425s Wrote p2-5_5-diagram.pdf 425s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 426s Treating sample p2-9_2 as female 435s Wrote p2-9_2-diagram.pdf 435s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 437s Treating sample p2-20_1 as female 445s Wrote p2-20_1-diagram.pdf 445s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 447s Treating sample p2-20_2 as female 454s Wrote p2-20_2-diagram.pdf 455s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 456s Treating sample p2-5_5 as female 456s Wrote p2-5_5-cbs-diagram.pdf 456s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 458s Treating sample p2-9_2 as female 458s Wrote p2-9_2-cbs-diagram.pdf 458s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 459s Treating sample p2-20_1 as female 460s Wrote p2-20_1-cbs-diagram.pdf 460s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 461s Treating sample p2-20_2 as female 462s Wrote p2-20_2-cbs-diagram.pdf 462s cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf 463s Treating sample p2-5_5 as female 468s Wrote p2-5_5-both-diagram.pdf 469s cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf 470s Treating sample p2-9_2 as female 476s Wrote p2-9_2-both-diagram.pdf 476s cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf 478s Treating sample p2-20_1 as female 483s Wrote p2-20_1-both-diagram.pdf 483s cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf 485s Treating sample p2-20_2 as female 490s Wrote p2-20_2-both-diagram.pdf 491s which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf 491s /usr/bin/pdfunite 491s cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf 492s Treating sample p2-5_5 as female 492s Treating sample p2-9_2 as female 492s Treating sample p2-20_1 as female 492s Treating sample p2-20_2 as female 492s Treating sample p2-20_3 as female 492s Treating sample p2-20_4 as female 492s Treating sample p2-20_5 as female 494s Wrote heatmap-picard.pdf 494s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 496s Found 14 gene breakpoints 496s Wrote p2-9_2-breaks.txt 496s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 498s Treating sample p2-9_2 as female 499s Found 323 gene-level gains and losses 499s Wrote p2-9_2-genemetrics.txt 499s cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt 501s Wrote gender-picard.txt 501s cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt 506s Wrote p2-all.cdt 506s cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt 511s Wrote p2-all-jtv.txt 511s cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg 512s Wrote p2-all.seg 513s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 514s Wrote p2-9_2.nexus 515s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 516s Selected test sample NA12882 and control sample NA12878 516s Loaded 3654 records; skipped: 514 somatic, 394 depth 516s Kept 2631 heterozygous of 3654 VCF records 519s Placed 705 variants into 18763 bins 519s Wrote p2-9_2.nexus-ogt 520s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 521s Treating sample p2-5_5 as female 521s Rescaling sample with purity 0.65, ploidy 2 521s Wrote build/p2-5_5.call.cns with 71 regions 521s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 523s Treating sample p2-9_2 as female 523s Rescaling sample with purity 0.65, ploidy 2 523s Wrote build/p2-9_2.call.cns with 103 regions 523s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 525s Treating sample p2-20_1 as female 525s Rescaling sample with purity 0.65, ploidy 2 525s Wrote build/p2-20_1.call.cns with 121 regions 529s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 529s Treating sample p2-20_2 as female 529s Rescaling sample with purity 0.65, ploidy 2 529s Wrote build/p2-20_2.call.cns with 117 regions 529s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 529s Treating sample p2-20_3 as female 529s Rescaling sample with purity 0.65, ploidy 2 529s Wrote build/p2-20_3.call.cns with 64 regions 529s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 530s Treating sample p2-20_4 as female 530s Rescaling sample with purity 0.65, ploidy 2 530s Wrote build/p2-20_4.call.cns with 143 regions 530s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 531s Treating sample p2-20_5 as female 531s Rescaling sample with purity 0.65, ploidy 2 531s Wrote build/p2-20_5.call.cns with 120 regions 532s cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed 533s Treating sample p2-5_5.call as female 533s Treating sample p2-9_2.call as female 533s Treating sample p2-20_1.call as female 533s Treating sample p2-20_2.call as female 533s Treating sample p2-20_3.call as female 533s Treating sample p2-20_4.call as female 533s Treating sample p2-20_5.call as female 533s Wrote p2-all.bed 533s cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf 535s Treating sample p2-9_2.call as female 535s Wrote p2-9_2.vcf 535s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 537s /usr/lib/python3/dist-packages/cnvlib/export.py:489: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 537s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 537s Wrote p2-9_2.theta2.input 537s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 537s --mean --median --mode --t-test \ 537s --stdev --mad --mse --iqr --bivar \ 537s --ci --pi --sem --smooth-bootstrap 540s Wrote p2-9_2-segmetrics.cns with 103 regions 540s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 540s --ci -b 50 -a 0.5 542s Wrote p2-5_5-segmetrics.cns with 71 regions 542s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 544s Wrote p2-5_5-metrics.tsv 544s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 546s Wrote p2-9_2-metrics.tsv 546s cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv 548s Wrote p2-20-metrics.tsv 548s PASS 548s autopkgtest [12:33:21]: test run-unit-test: -----------------------] 645s autopkgtest [12:34:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 645s run-unit-test PASS 664s autopkgtest [12:35:17]: test pybuild-autopkgtest: preparing testbed 889s Note, using file '/tmp/autopkgtest.lQrRjI/3-autopkgtest-satdep.dsc' to get the build dependencies 889s Reading package lists... 889s Building dependency tree... 889s Reading state information... 889s Starting pkgProblemResolver with broken count: 0 889s Starting 2 pkgProblemResolver with broken count: 0 889s Done 890s The following NEW packages will be installed: 890s autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf 890s dh-python dh-strip-nondeterminism dwz gettext intltool-debian 890s libarchive-zip-perl libdebhelper-perl libfile-stripnondeterminism-perl 890s libpython3.13-minimal libpython3.13-stdlib libtool m4 po-debconf 890s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python3-all 890s python3-build python3-iniconfig python3-installer python3-pluggy 890s python3-pyproject-hooks python3-pytest python3-toml python3-wheel python3.13 890s python3.13-minimal 897s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 897s Need to get 10.9 MB of archives. 897s After this operation, 37.5 MB of additional disk space will be used. 897s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 897s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 897s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 897s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 897s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 897s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 897s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 897s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 897s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 897s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 897s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 897s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 897s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 897s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 897s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 897s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 897s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 897s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 897s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 897s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 897s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 897s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 897s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 897s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 897s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.44.0-1 [54.2 kB] 897s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 897s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 897s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 897s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 897s Get:30 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 897s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 897s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 897s Get:33 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 897s Fetched 10.9 MB in 0s (29.0 MB/s) 897s Selecting previously unselected package libpython3.13-minimal:amd64. 897s (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 ... 94066 files and directories currently installed.) 897s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 897s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 897s Selecting previously unselected package python3.13-minimal. 897s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 897s Unpacking python3.13-minimal (3.13.0-2) ... 897s Selecting previously unselected package m4. 897s Preparing to unpack .../02-m4_1.4.19-4build1_amd64.deb ... 897s Unpacking m4 (1.4.19-4build1) ... 897s Selecting previously unselected package autoconf. 897s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 897s Unpacking autoconf (2.72-3) ... 897s Selecting previously unselected package autotools-dev. 897s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 897s Unpacking autotools-dev (20220109.1) ... 897s Selecting previously unselected package automake. 897s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 897s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 897s Selecting previously unselected package autopoint. 897s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 897s Unpacking autopoint (0.22.5-2) ... 897s Selecting previously unselected package libdebhelper-perl. 897s Preparing to unpack .../07-libdebhelper-perl_13.20ubuntu1_all.deb ... 897s Unpacking libdebhelper-perl (13.20ubuntu1) ... 897s Selecting previously unselected package libtool. 897s Preparing to unpack .../08-libtool_2.4.7-7build1_all.deb ... 897s Unpacking libtool (2.4.7-7build1) ... 897s Selecting previously unselected package dh-autoreconf. 897s Preparing to unpack .../09-dh-autoreconf_20_all.deb ... 897s Unpacking dh-autoreconf (20) ... 897s Selecting previously unselected package libarchive-zip-perl. 897s Preparing to unpack .../10-libarchive-zip-perl_1.68-1_all.deb ... 897s Unpacking libarchive-zip-perl (1.68-1) ... 897s Selecting previously unselected package libfile-stripnondeterminism-perl. 897s Preparing to unpack .../11-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... 897s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... 897s Selecting previously unselected package dh-strip-nondeterminism. 897s Preparing to unpack .../12-dh-strip-nondeterminism_1.14.0-1_all.deb ... 897s Unpacking dh-strip-nondeterminism (1.14.0-1) ... 897s Selecting previously unselected package debugedit. 897s Preparing to unpack .../13-debugedit_1%3a5.1-1_amd64.deb ... 897s Unpacking debugedit (1:5.1-1) ... 897s Selecting previously unselected package dwz. 897s Preparing to unpack .../14-dwz_0.15-1build6_amd64.deb ... 897s Unpacking dwz (0.15-1build6) ... 897s Selecting previously unselected package gettext. 897s Preparing to unpack .../15-gettext_0.22.5-2_amd64.deb ... 897s Unpacking gettext (0.22.5-2) ... 897s Selecting previously unselected package intltool-debian. 897s Preparing to unpack .../16-intltool-debian_0.35.0+20060710.6_all.deb ... 897s Unpacking intltool-debian (0.35.0+20060710.6) ... 897s Selecting previously unselected package po-debconf. 897s Preparing to unpack .../17-po-debconf_1.0.21+nmu1_all.deb ... 897s Unpacking po-debconf (1.0.21+nmu1) ... 897s Selecting previously unselected package debhelper. 897s Preparing to unpack .../18-debhelper_13.20ubuntu1_all.deb ... 897s Unpacking debhelper (13.20ubuntu1) ... 897s Selecting previously unselected package dh-python. 897s Preparing to unpack .../19-dh-python_6.20241024_all.deb ... 897s Unpacking dh-python (6.20241024) ... 897s Selecting previously unselected package libpython3.13-stdlib:amd64. 897s Preparing to unpack .../20-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 897s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 897s Selecting previously unselected package pybuild-plugin-autopkgtest. 897s Preparing to unpack .../21-pybuild-plugin-autopkgtest_6.20241024_all.deb ... 897s Unpacking pybuild-plugin-autopkgtest (6.20241024) ... 897s Selecting previously unselected package python3-pyproject-hooks. 897s Preparing to unpack .../22-python3-pyproject-hooks_1.2.0-1_all.deb ... 897s Unpacking python3-pyproject-hooks (1.2.0-1) ... 897s Selecting previously unselected package python3-toml. 897s Preparing to unpack .../23-python3-toml_0.10.2-1_all.deb ... 897s Unpacking python3-toml (0.10.2-1) ... 897s Selecting previously unselected package python3-wheel. 897s Preparing to unpack .../24-python3-wheel_0.44.0-1_all.deb ... 897s Unpacking python3-wheel (0.44.0-1) ... 897s Selecting previously unselected package python3-build. 897s Preparing to unpack .../25-python3-build_1.2.2-1_all.deb ... 897s Unpacking python3-build (1.2.2-1) ... 897s Selecting previously unselected package python3-installer. 897s Preparing to unpack .../26-python3-installer_0.7.0+dfsg1-3_all.deb ... 897s Unpacking python3-installer (0.7.0+dfsg1-3) ... 897s Selecting previously unselected package pybuild-plugin-pyproject. 897s Preparing to unpack .../27-pybuild-plugin-pyproject_6.20241024_all.deb ... 897s Unpacking pybuild-plugin-pyproject (6.20241024) ... 897s Selecting previously unselected package python3.13. 897s Preparing to unpack .../28-python3.13_3.13.0-2_amd64.deb ... 897s Unpacking python3.13 (3.13.0-2) ... 897s Selecting previously unselected package python3-all. 897s Preparing to unpack .../29-python3-all_3.12.7-1_amd64.deb ... 897s Unpacking python3-all (3.12.7-1) ... 897s Selecting previously unselected package python3-iniconfig. 897s Preparing to unpack .../30-python3-iniconfig_1.1.1-2_all.deb ... 897s Unpacking python3-iniconfig (1.1.1-2) ... 897s Selecting previously unselected package python3-pluggy. 897s Preparing to unpack .../31-python3-pluggy_1.5.0-1_all.deb ... 897s Unpacking python3-pluggy (1.5.0-1) ... 897s Selecting previously unselected package python3-pytest. 897s Preparing to unpack .../32-python3-pytest_8.3.3-1_all.deb ... 897s Unpacking python3-pytest (8.3.3-1) ... 897s Setting up dh-python (6.20241024) ... 897s Setting up python3-iniconfig (1.1.1-2) ... 897s Setting up gettext (0.22.5-2) ... 897s Setting up libarchive-zip-perl (1.68-1) ... 897s Setting up libdebhelper-perl (13.20ubuntu1) ... 897s Setting up m4 (1.4.19-4build1) ... 897s Setting up python3-wheel (0.44.0-1) ... 897s Setting up intltool-debian (0.35.0+20060710.6) ... 897s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 897s Setting up autotools-dev (20220109.1) ... 897s Setting up python3-pyproject-hooks (1.2.0-1) ... 897s Setting up autopoint (0.22.5-2) ... 897s Setting up python3-toml (0.10.2-1) ... 897s Setting up python3-installer (0.7.0+dfsg1-3) ... 897s Setting up autoconf (2.72-3) ... 897s Setting up python3-pluggy (1.5.0-1) ... 897s Setting up dwz (0.15-1build6) ... 897s Setting up debugedit (1:5.1-1) ... 897s Setting up python3.13-minimal (3.13.0-2) ... 897s Setting up python3-build (1.2.2-1) ... 897s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 897s Setting up automake (1:1.16.5-1.3ubuntu1) ... 897s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 897s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 897s Setting up libtool (2.4.7-7build1) ... 897s Setting up python3.13 (3.13.0-2) ... 897s Setting up pybuild-plugin-pyproject (6.20241024) ... 897s Setting up python3-pytest (8.3.3-1) ... 897s Setting up po-debconf (1.0.21+nmu1) ... 897s Setting up python3-all (3.12.7-1) ... 897s Setting up dh-autoreconf (20) ... 897s Setting up dh-strip-nondeterminism (1.14.0-1) ... 897s Setting up debhelper (13.20ubuntu1) ... 897s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 897s Processing triggers for man-db (2.12.1-3) ... 897s Processing triggers for install-info (7.1.1-1) ... 897s Processing triggers for libc-bin (2.40-1ubuntu3) ... 897s Processing triggers for systemd (256.5-2ubuntu4) ... 903s Reading package lists... 904s Building dependency tree... 904s Reading state information... 904s Starting pkgProblemResolver with broken count: 0 904s Starting 2 pkgProblemResolver with broken count: 0 904s Done 904s The following NEW packages will be installed: 904s autopkgtest-satdep 904s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 904s Need to get 0 B/696 B of archives. 904s After this operation, 0 B of additional disk space will be used. 904s Get:1 /tmp/autopkgtest.lQrRjI/4-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 905s Selecting previously unselected package autopkgtest-satdep. 905s (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 ... 96203 files and directories currently installed.) 905s Preparing to unpack .../4-autopkgtest-satdep.deb ... 905s Unpacking autopkgtest-satdep (0) ... 905s Setting up autopkgtest-satdep (0) ... 947s (Reading database ... 96203 files and directories currently installed.) 947s Removing autopkgtest-satdep (0) ... 978s autopkgtest [12:40:31]: test pybuild-autopkgtest: pybuild-autopkgtest 978s autopkgtest [12:40:31]: test pybuild-autopkgtest: [----------------------- 979s pybuild-autopkgtest 979s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.lQrRjI/build.W1q/src/data /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/data; 980s I: pybuild base:311: cd /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build; python3.13 -m pytest test 980s ============================= test session starts ============================== 980s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 980s rootdir: /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build 980s configfile: pyproject.toml 980s plugins: typeguard-4.4.1 980s collected 0 items / 5 errors 980s 980s ==================================== ERRORS ==================================== 980s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 980s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_cnvlib.py'. 980s Hint: make sure your test modules/packages have valid Python names. 980s Traceback: 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 980s from . import multiarray 980s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 980s from . import overrides 980s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 980s from numpy.core._multiarray_umath import ( 980s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 980s 980s During handling of the above exception, another exception occurred: 980s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 980s from numpy.__config__ import show as show_config 980s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 980s from numpy.core._multiarray_umath import ( 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 980s raise ImportError(msg) 980s E ImportError: 980s E 980s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 980s E 980s E Importing the numpy C-extensions failed. This error can happen for 980s E many reasons, often due to issues with your setup or how NumPy was 980s E installed. 980s E 980s E We have compiled some common reasons and troubleshooting tips at: 980s E 980s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 980s E 980s E Please note and check the following: 980s E 980s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 980s E * The NumPy version is: "1.26.4" 980s E 980s E and make sure that they are the versions you expect. 980s E Please carefully study the documentation linked above for further help. 980s E 980s E Original error was: No module named 'numpy.core._multiarray_umath' 980s 980s The above exception was the direct cause of the following exception: 980s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 980s return _bootstrap._gcd_import(name[level:], package, level) 980s test/test_cnvlib.py:15: in 980s import numpy as np 980s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 980s raise ImportError(msg) from e 980s E ImportError: Error importing numpy: you should not try to import numpy from 980s E its source directory; please exit the numpy source tree, and relaunch 980s E your python interpreter from there. 980s ____________________ ERROR collecting test/test_commands.py ____________________ 980s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_commands.py'. 980s Hint: make sure your test modules/packages have valid Python names. 980s Traceback: 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 980s from . import multiarray 980s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 980s from . import overrides 980s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 980s from numpy.core._multiarray_umath import ( 980s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 980s 980s During handling of the above exception, another exception occurred: 980s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 980s from numpy.__config__ import show as show_config 980s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 980s from numpy.core._multiarray_umath import ( 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 980s raise ImportError(msg) 980s E ImportError: 980s E 980s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 980s E 980s E Importing the numpy C-extensions failed. This error can happen for 980s E many reasons, often due to issues with your setup or how NumPy was 980s E installed. 980s E 980s E We have compiled some common reasons and troubleshooting tips at: 980s E 980s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 980s E 980s E Please note and check the following: 980s E 980s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 980s E * The NumPy version is: "1.26.4" 980s E 980s E and make sure that they are the versions you expect. 980s E Please carefully study the documentation linked above for further help. 980s E 980s E Original error was: No module named 'numpy.core._multiarray_umath' 980s 980s The above exception was the direct cause of the following exception: 980s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 980s return _bootstrap._gcd_import(name[level:], package, level) 980s test/test_commands.py:16: in 980s import numpy as np 980s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 980s raise ImportError(msg) from e 980s E ImportError: Error importing numpy: you should not try to import numpy from 980s E its source directory; please exit the numpy source tree, and relaunch 980s E your python interpreter from there. 980s _____________________ ERROR collecting test/test_genome.py _____________________ 980s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_genome.py'. 980s Hint: make sure your test modules/packages have valid Python names. 980s Traceback: 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 980s from . import multiarray 980s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 980s from . import overrides 980s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 980s from numpy.core._multiarray_umath import ( 980s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 980s 980s During handling of the above exception, another exception occurred: 980s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 980s from numpy.__config__ import show as show_config 980s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 980s from numpy.core._multiarray_umath import ( 980s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 980s raise ImportError(msg) 980s E ImportError: 980s E 980s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 980s E 980s E Importing the numpy C-extensions failed. This error can happen for 980s E many reasons, often due to issues with your setup or how NumPy was 980s E installed. 980s E 980s E We have compiled some common reasons and troubleshooting tips at: 980s E 980s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 980s E 980s E Please note and check the following: 980s E 980s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 980s E * The NumPy version is: "1.26.4" 980s E 980s E and make sure that they are the versions you expect. 980s E Please carefully study the documentation linked above for further help. 980s E 980s E Original error was: No module named 'numpy.core._multiarray_umath' 980s 980s The above exception was the direct cause of the following exception: 980s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 980s return _bootstrap._gcd_import(name[level:], package, level) 980s test/test_genome.py:12: in 980s import numpy as np 980s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 980s raise ImportError(msg) from e 980s E ImportError: Error importing numpy: you should not try to import numpy from 980s E its source directory; please exit the numpy source tree, and relaunch 980s E your python interpreter from there. 980s _______________________ ERROR collecting test/test_io.py _______________________ 980s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_io.py'. 980s Hint: make sure your test modules/packages have valid Python names. 980s Traceback: 980s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 980s return _bootstrap._gcd_import(name[level:], package, level) 980s test/test_io.py:11: in 980s from skgenome import tabio 980s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 980s from . import tabio 980s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 980s import pandas as pd 980s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 980s raise ImportError( 980s E ImportError: Unable to import required dependencies: 980s E numpy: Error importing numpy: you should not try to import numpy from 980s E its source directory; please exit the numpy source tree, and relaunch 980s E your python interpreter from there. 980s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 980s _______________________ ERROR collecting test/test_r.py ________________________ 980s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_r.py'. 980s Hint: make sure your test modules/packages have valid Python names. 980s Traceback: 980s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 980s return _bootstrap._gcd_import(name[level:], package, level) 980s test/test_r.py:14: in 980s import cnvlib 980s /usr/lib/python3/dist-packages/cnvlib/__init__.py:1: in 980s from skgenome.tabio import write 980s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 980s from . import tabio 980s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 980s import pandas as pd 980s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 980s raise ImportError( 980s E ImportError: Unable to import required dependencies: 980s E numpy: Error importing numpy: you should not try to import numpy from 980s E its source directory; please exit the numpy source tree, and relaunch 980s E your python interpreter from there. 980s =========================== short test summary info ============================ 980s ERROR test/test_cnvlib.py 980s ERROR test/test_commands.py 980s ERROR test/test_genome.py 980s ERROR test/test_io.py 980s ERROR test/test_r.py 980s !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! 980s ============================== 5 errors in 0.31s =============================== 980s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build; python3.13 -m pytest test 980s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.lQrRjI/build.W1q/src/data /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/data; 980s I: pybuild base:311: cd /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build; python3.12 -m pytest test 983s ============================= test session starts ============================== 983s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 983s rootdir: /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build 983s configfile: pyproject.toml 983s plugins: typeguard-4.4.1 983s collected 55 items / 1 error 983s 983s ==================================== ERRORS ==================================== 983s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 983s ImportError while importing test module '/tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build/test/test_cnvlib.py'. 983s Hint: make sure your test modules/packages have valid Python names. 983s Traceback: 983s /usr/lib/python3.12/importlib/__init__.py:90: in import_module 983s return _bootstrap._gcd_import(name[level:], package, level) 983s test/test_cnvlib.py:16: in 983s from skgenome import GenomicArray, tabio 983s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 983s from . import tabio 983s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 983s import pandas as pd 983s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 983s raise ImportError( 983s E ImportError: Unable to import required dependencies: 983s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 983s =========================== short test summary info ============================ 983s ERROR test/test_cnvlib.py 983s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 983s =============================== 1 error in 2.49s =============================== 983s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.lQrRjI/autopkgtest_tmp/build; python3.12 -m pytest test 983s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 983s make: *** [/tmp/izKhaFyhPg/run:4: pybuild-autopkgtest] Error 25 983s pybuild-autopkgtest: error: /tmp/izKhaFyhPg/run pybuild-autopkgtest returned exit code 2 984s autopkgtest [12:40:37]: test pybuild-autopkgtest: -----------------------] 984s pybuild-autopkgtest FAIL non-zero exit status 25 984s autopkgtest [12:40:37]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 989s autopkgtest [12:40:42]: @@@@@@@@@@@@@@@@@@@@ summary 989s run-unit-test PASS 989s pybuild-autopkgtest FAIL non-zero exit status 25 1170s virt: nova [W] Skipping flock for amd64 1170s virt: Creating nova instance adt-plucky-i386-cnvkit-20241113-122413-juju-7f2275-prod-proposed-migration-environment-2-cc351134-859e-4525-8038-108608b1b304 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...