0s autopkgtest [01:26:59]: starting date and time: 2025-03-16 01:26:59+0000 0s autopkgtest [01:26:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:26:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2hig8eg_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-27.secgroup --name adt-plucky-arm64-cnvkit-20250316-012658-juju-7f2275-prod-proposed-migration-environment-2-9f5d3358-6796-4d12-a882-bf9375edc1cd --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 108s autopkgtest [01:28:47]: testbed dpkg architecture: arm64 108s autopkgtest [01:28:47]: testbed apt version: 2.9.33 109s autopkgtest [01:28:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 109s autopkgtest [01:28:48]: testbed release detected to be: None 110s autopkgtest [01:28:49]: updating testbed package index (apt update) 110s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 110s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 111s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 111s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 111s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 111s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 111s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [72.2 kB] 111s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1816 B] 111s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 111s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [316 kB] 111s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [13.9 kB] 111s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [16.8 kB] 111s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 111s Fetched 972 kB in 1s (847 kB/s) 113s Reading package lists... 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Calculating upgrade... 115s Calculating upgrade... 115s The following packages will be upgraded: 115s pinentry-curses python3-jinja2 strace 115s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 647 kB of archives. 115s After this operation, 11.3 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 116s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 117s Fetched 647 kB in 1s (947 kB/s) 117s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 117s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 117s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 117s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 117s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 117s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 117s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 117s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 117s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 118s Setting up strace (6.13+ds-1ubuntu1) ... 118s Processing triggers for man-db (2.13.0-1) ... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Solving dependencies... 120s The following packages will be REMOVED: 120s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 120s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 120s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 120s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 120s 0 upgraded, 0 newly installed, 11 to remove and 0 not upgraded. 120s After this operation, 267 MB disk space will be freed. 120s (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 ... 117701 files and directories currently installed.) 120s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 120s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 120s Removing libpython3.12t64:arm64 (3.12.9-1) ... 120s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 120s Removing libnsl2:arm64 (1.3.0-3build3) ... 120s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 121s Removing libunwind8:arm64 (1.6.2-3.1) ... 121s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 121s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 123s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 123s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 123s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 123s /etc/kernel/postrm.d/initramfs-tools: 123s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 124s /etc/kernel/postrm.d/zz-flash-kernel: 124s flash-kernel: Kernel 6.11.0-8-generic has been removed. 124s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 124s /etc/kernel/postrm.d/zz-update-grub: 124s Sourcing file `/etc/default/grub' 124s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 124s Generating grub configuration file ... 124s Found linux image: /boot/vmlinuz-6.14.0-10-generic 124s Found initrd image: /boot/initrd.img-6.14.0-10-generic 124s Warning: os-prober will not be executed to detect other bootable partitions. 124s Systems on them will not be added to the GRUB boot configuration. 124s Check GRUB_DISABLE_OS_PROBER documentation entry. 124s Adding boot menu entry for UEFI Firmware Settings ... 125s done 125s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 125s Processing triggers for libc-bin (2.41-1ubuntu1) ... 125s (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 ... 81650 files and directories currently installed.) 125s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 125s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 125s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 125s autopkgtest [01:29:04]: upgrading testbed (apt dist-upgrade and autopurge) 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 127s Entering ResolveByKeep 128s 128s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 129s Solving dependencies... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [01:29:09]: rebooting testbed after setup commands that affected boot 154s autopkgtest [01:29:33]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 157s autopkgtest [01:29:36]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 168s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (dsc) [2483 B] 168s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (tar) [32.1 MB] 168s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (diff) [20.8 kB] 169s gpgv: Signature made Thu Feb 6 14:25:04 2025 UTC 169s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 169s gpgv: issuer "crusoe@debian.org" 169s gpgv: Can't check signature: No public key 169s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.12-1.dsc: no acceptable signature found 170s autopkgtest [01:29:49]: testing package cnvkit version 0.9.12-1 170s autopkgtest [01:29:49]: build not needed 175s autopkgtest [01:29:54]: test run-unit-test: preparing testbed 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Starting pkgProblemResolver with broken count: 0 176s Starting 2 pkgProblemResolver with broken count: 0 176s Done 177s The following NEW packages will be installed: 177s blt cnvkit cython3 fontconfig fontconfig-config fonts-dejavu-core 177s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 177s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgpgmepp6t64 177s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 177s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 177s liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 177s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 177s libpoppler147 libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 177s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 177s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 177s poppler-utils python-matplotlib-data python3-biopython python3-brotli 177s python3-cairo python3-contourpy python3-cycler python3-dateutil 177s python3-decorator python3-fonttools python3-freetype python3-fs 177s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 177s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 177s python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib 177s python3-pil python3-pil.imagetk python3-platformdirs python3-pomegranate 177s python3-pyfaidx python3-pysam python3-pytz python3-reportlab 177s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 177s python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 177s python3-unicodedata2 python3.12-tk python3.13-tk r-base-core 177s r-bioc-biocgenerics r-bioc-dnacopy sgml-base tk8.6-blt2.5 unicode-data unzip 177s w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 177s 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. 177s Need to get 174 MB of archives. 177s After this operation, 729 MB of additional disk space will be used. 177s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 178s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 178s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 179s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 180s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 180s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 180s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 180s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 180s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 180s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 180s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 181s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 181s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 184s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 184s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 184s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 184s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 184s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 184s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 184s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 184s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 184s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 184s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 184s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 184s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 184s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 184s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 185s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 185s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 185s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 185s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 185s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 185s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 185s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 185s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 185s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 185s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 185s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 185s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 185s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 185s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 185s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 185s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 185s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 185s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 185s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 185s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 186s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build2 [122 kB] 186s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 186s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 186s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 186s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 186s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 186s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 187s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 187s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 187s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 187s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 188s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 188s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 188s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 188s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 188s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 188s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 188s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 188s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 188s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 188s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 188s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 188s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 193s Get:72 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 194s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 195s Get:74 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 195s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build3 [360 kB] 195s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 198s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 198s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 198s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 198s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 198s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 204s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 204s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 204s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 205s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 206s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu2 [2436 kB] 207s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-3 [205 kB] 207s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 211s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pomegranate arm64 0.15.0-1build1 [3013 kB] 212s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 212s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 212s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 212s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 212s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 213s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 213s Get:96 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 214s Get:97 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 215s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 215s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 215s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 215s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 215s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 215s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 216s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 216s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 216s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 216s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 216s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 216s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 216s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 216s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 216s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 217s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 232s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 232s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-dnacopy arm64 1.80.0-2 [497 kB] 233s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 cnvkit all 0.9.12-1 [20.6 MB] 244s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgmepp6t64 arm64 1.24.2-1ubuntu2 [119 kB] 244s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libpoppler147 arm64 25.03.0-2 [1154 kB] 245s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-utils arm64 25.03.0-2 [212 kB] 245s Preconfiguring packages ... 246s Fetched 174 MB in 1min 8s (2568 kB/s) 246s Selecting previously unselected package python3-numpy-dev:arm64. 246s (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 ... 81647 files and directories currently installed.) 246s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 246s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 246s Selecting previously unselected package libblas3:arm64. 246s Preparing to unpack .../001-libblas3_3.12.1-2_arm64.deb ... 246s Unpacking libblas3:arm64 (3.12.1-2) ... 246s Selecting previously unselected package libgfortran5:arm64. 246s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 246s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 246s Selecting previously unselected package liblapack3:arm64. 246s Preparing to unpack .../003-liblapack3_3.12.1-2_arm64.deb ... 246s Unpacking liblapack3:arm64 (3.12.1-2) ... 246s Selecting previously unselected package python3-numpy. 246s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 246s Unpacking python3-numpy (1:2.2.3+ds-5) ... 246s Selecting previously unselected package sgml-base. 246s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 246s Unpacking sgml-base (1.31) ... 246s Selecting previously unselected package libtcl8.6:arm64. 246s Preparing to unpack .../006-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 246s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 246s Selecting previously unselected package fonts-dejavu-mono. 246s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... 246s Unpacking fonts-dejavu-mono (2.37-8) ... 246s Selecting previously unselected package fonts-dejavu-core. 246s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... 246s Unpacking fonts-dejavu-core (2.37-8) ... 246s Selecting previously unselected package libfontenc1:arm64. 246s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 246s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 246s Selecting previously unselected package x11-common. 246s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 246s Unpacking x11-common (1:7.7+23ubuntu3) ... 247s Selecting previously unselected package xfonts-encodings. 247s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 247s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 247s Selecting previously unselected package xfonts-utils. 247s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_arm64.deb ... 247s Unpacking xfonts-utils (1:7.7+7) ... 247s Selecting previously unselected package fonts-urw-base35. 247s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ... 247s Unpacking fonts-urw-base35 (20200910-8) ... 247s Selecting previously unselected package fontconfig-config. 247s Preparing to unpack .../014-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 247s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 247s Selecting previously unselected package libfontconfig1:arm64. 247s Preparing to unpack .../015-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 247s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 247s Selecting previously unselected package libxrender1:arm64. 247s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 247s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 247s Selecting previously unselected package libxft2:arm64. 247s Preparing to unpack .../017-libxft2_2.3.6-1build1_arm64.deb ... 247s Unpacking libxft2:arm64 (2.3.6-1build1) ... 247s Selecting previously unselected package libxss1:arm64. 247s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_arm64.deb ... 247s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 247s Selecting previously unselected package libtk8.6:arm64. 247s Preparing to unpack .../019-libtk8.6_8.6.16-1_arm64.deb ... 247s Unpacking libtk8.6:arm64 (8.6.16-1) ... 247s Selecting previously unselected package tk8.6-blt2.5. 247s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 247s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 247s Selecting previously unselected package blt. 247s Preparing to unpack .../021-blt_2.5.3+dfsg-8_arm64.deb ... 247s Unpacking blt (2.5.3+dfsg-8) ... 247s Selecting previously unselected package python3.12-tk. 247s Preparing to unpack .../022-python3.12-tk_3.12.9-1_arm64.deb ... 247s Unpacking python3.12-tk (3.12.9-1) ... 247s Selecting previously unselected package python3.13-tk. 247s Preparing to unpack .../023-python3.13-tk_3.13.2-2_arm64.deb ... 247s Unpacking python3.13-tk (3.13.2-2) ... 247s Selecting previously unselected package python3-tk:arm64. 248s Preparing to unpack .../024-python3-tk_3.13.1-1_arm64.deb ... 248s Unpacking python3-tk:arm64 (3.13.1-1) ... 248s Selecting previously unselected package python3-pil.imagetk:arm64. 248s Preparing to unpack .../025-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 248s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 248s Selecting previously unselected package libgomp1:arm64. 248s Preparing to unpack .../026-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 248s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 248s Selecting previously unselected package libimagequant0:arm64. 248s Preparing to unpack .../027-libimagequant0_2.18.0-1build1_arm64.deb ... 248s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 248s Selecting previously unselected package libjpeg-turbo8:arm64. 248s Preparing to unpack .../028-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 248s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 248s Selecting previously unselected package libjpeg8:arm64. 248s Preparing to unpack .../029-libjpeg8_8c-2ubuntu11_arm64.deb ... 248s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 248s Selecting previously unselected package liblcms2-2:arm64. 248s Preparing to unpack .../030-liblcms2-2_2.16-2_arm64.deb ... 248s Unpacking liblcms2-2:arm64 (2.16-2) ... 248s Selecting previously unselected package libopenjp2-7:arm64. 248s Preparing to unpack .../031-libopenjp2-7_2.5.3-2_arm64.deb ... 248s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 248s Selecting previously unselected package libgraphite2-3:arm64. 248s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 248s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 248s Selecting previously unselected package libharfbuzz0b:arm64. 248s Preparing to unpack .../033-libharfbuzz0b_10.2.0-1_arm64.deb ... 248s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 248s Selecting previously unselected package libraqm0:arm64. 248s Preparing to unpack .../034-libraqm0_0.10.2-1_arm64.deb ... 248s Unpacking libraqm0:arm64 (0.10.2-1) ... 248s Selecting previously unselected package libdeflate0:arm64. 248s Preparing to unpack .../035-libdeflate0_1.23-1_arm64.deb ... 248s Unpacking libdeflate0:arm64 (1.23-1) ... 248s Selecting previously unselected package libjbig0:arm64. 248s Preparing to unpack .../036-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 248s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 248s Selecting previously unselected package liblerc4:arm64. 248s Preparing to unpack .../037-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 248s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 248s Selecting previously unselected package libsharpyuv0:arm64. 248s Preparing to unpack .../038-libsharpyuv0_1.5.0-0.1_arm64.deb ... 248s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 248s Selecting previously unselected package libwebp7:arm64. 248s Preparing to unpack .../039-libwebp7_1.5.0-0.1_arm64.deb ... 248s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 248s Selecting previously unselected package libtiff6:arm64. 248s Preparing to unpack .../040-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 248s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 248s Selecting previously unselected package libwebpdemux2:arm64. 248s Preparing to unpack .../041-libwebpdemux2_1.5.0-0.1_arm64.deb ... 248s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 248s Selecting previously unselected package libwebpmux3:arm64. 248s Preparing to unpack .../042-libwebpmux3_1.5.0-0.1_arm64.deb ... 248s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 248s Selecting previously unselected package python3-pil:arm64. 248s Preparing to unpack .../043-python3-pil_11.1.0-5build1_arm64.deb ... 248s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 248s Selecting previously unselected package libpixman-1-0:arm64. 248s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_arm64.deb ... 248s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 248s Selecting previously unselected package libxcb-render0:arm64. 248s Preparing to unpack .../045-libxcb-render0_1.17.0-2_arm64.deb ... 248s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 248s Selecting previously unselected package libxcb-shm0:arm64. 248s Preparing to unpack .../046-libxcb-shm0_1.17.0-2_arm64.deb ... 248s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 248s Selecting previously unselected package libcairo2:arm64. 248s Preparing to unpack .../047-libcairo2_1.18.2-2_arm64.deb ... 248s Unpacking libcairo2:arm64 (1.18.2-2) ... 248s Selecting previously unselected package python3-cairo. 248s Preparing to unpack .../048-python3-cairo_1.26.1-2build2_arm64.deb ... 248s Unpacking python3-cairo (1.26.1-2build2) ... 248s Selecting previously unselected package python3-freetype. 248s Preparing to unpack .../049-python3-freetype_2.5.1-1_all.deb ... 248s Unpacking python3-freetype (2.5.1-1) ... 248s Selecting previously unselected package python3-rlpycairo. 248s Preparing to unpack .../050-python3-rlpycairo_0.3.0-3_all.deb ... 248s Unpacking python3-rlpycairo (0.3.0-3) ... 248s Selecting previously unselected package python3-reportlab. 249s Preparing to unpack .../051-python3-reportlab_4.3.1-1_all.deb ... 249s Unpacking python3-reportlab (4.3.1-1) ... 249s Selecting previously unselected package xml-core. 249s Preparing to unpack .../052-xml-core_0.19_all.deb ... 249s Unpacking xml-core (0.19) ... 249s Selecting previously unselected package w3c-sgml-lib. 249s Preparing to unpack .../053-w3c-sgml-lib_1.3-3_all.deb ... 249s Unpacking w3c-sgml-lib (1.3-3) ... 249s Selecting previously unselected package python3-biopython. 249s Preparing to unpack .../054-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 249s Unpacking python3-biopython (1.85+dfsg-2build1) ... 249s Selecting previously unselected package libjs-jquery. 249s Preparing to unpack .../055-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 249s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 249s Selecting previously unselected package libjs-jquery-ui. 249s Preparing to unpack .../056-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 249s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 249s Selecting previously unselected package fonts-lyx. 249s Preparing to unpack .../057-fonts-lyx_2.4.3-1_all.deb ... 249s Unpacking fonts-lyx (2.4.3-1) ... 249s Selecting previously unselected package python-matplotlib-data. 249s Preparing to unpack .../058-python-matplotlib-data_3.8.3-7build1_all.deb ... 249s Unpacking python-matplotlib-data (3.8.3-7build1) ... 249s Selecting previously unselected package python3-dateutil. 249s Preparing to unpack .../059-python3-dateutil_2.9.0-3_all.deb ... 249s Unpacking python3-dateutil (2.9.0-3) ... 249s Selecting previously unselected package python3-contourpy. 249s Preparing to unpack .../060-python3-contourpy_1.3.1-1build1_arm64.deb ... 249s Unpacking python3-contourpy (1.3.1-1build1) ... 249s Selecting previously unselected package python3-cycler. 249s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 249s Unpacking python3-cycler (0.12.1-1) ... 249s Selecting previously unselected package python3-brotli. 249s Preparing to unpack .../062-python3-brotli_1.1.0-2build4_arm64.deb ... 249s Unpacking python3-brotli (1.1.0-2build4) ... 249s Selecting previously unselected package python3-platformdirs. 249s Preparing to unpack .../063-python3-platformdirs_4.3.6-1_all.deb ... 249s Unpacking python3-platformdirs (4.3.6-1) ... 249s Selecting previously unselected package python3-fs. 249s Preparing to unpack .../064-python3-fs_2.4.16-7_all.deb ... 249s Unpacking python3-fs (2.4.16-7) ... 249s Selecting previously unselected package libxslt1.1:arm64. 249s Preparing to unpack .../065-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 249s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 249s Selecting previously unselected package python3-lxml:arm64. 249s Preparing to unpack .../066-python3-lxml_5.3.1-1build1_arm64.deb ... 249s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 249s Selecting previously unselected package python3-lz4. 249s Preparing to unpack .../067-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 249s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 249s Selecting previously unselected package python3-decorator. 249s Preparing to unpack .../068-python3-decorator_5.1.1-5_all.deb ... 249s Unpacking python3-decorator (5.1.1-5) ... 250s Selecting previously unselected package liblbfgsb0:arm64. 250s Preparing to unpack .../069-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 250s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 250s Selecting previously unselected package python3-scipy. 250s Preparing to unpack .../070-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 250s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 250s Selecting previously unselected package python3-mpmath. 250s Preparing to unpack .../071-python3-mpmath_1.3.0-1_all.deb ... 250s Unpacking python3-mpmath (1.3.0-1) ... 250s Selecting previously unselected package python3-sympy. 250s Preparing to unpack .../072-python3-sympy_1.13.3-5_all.deb ... 250s Unpacking python3-sympy (1.13.3-5) ... 250s Selecting previously unselected package python3-ufolib2. 250s Preparing to unpack .../073-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 250s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 250s Selecting previously unselected package python3-unicodedata2. 250s Preparing to unpack .../074-python3-unicodedata2_15.1.0+ds-1build3_arm64.deb ... 250s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 250s Selecting previously unselected package unicode-data. 250s Preparing to unpack .../075-unicode-data_15.1.0-1_all.deb ... 250s Unpacking unicode-data (15.1.0-1) ... 251s Selecting previously unselected package python3-fonttools. 251s Preparing to unpack .../076-python3-fonttools_4.55.3-2build1_arm64.deb ... 251s Unpacking python3-fonttools (4.55.3-2build1) ... 251s Selecting previously unselected package python3-kiwisolver. 251s Preparing to unpack .../077-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 251s Unpacking python3-kiwisolver (1.4.7-3build1) ... 251s Selecting previously unselected package python3-packaging. 251s Preparing to unpack .../078-python3-packaging_24.2-1_all.deb ... 251s Unpacking python3-packaging (24.2-1) ... 251s Selecting previously unselected package libqhull-r8.0:arm64. 251s Preparing to unpack .../079-libqhull-r8.0_2020.2-6build1_arm64.deb ... 251s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 251s Selecting previously unselected package python3-matplotlib. 251s Preparing to unpack .../080-python3-matplotlib_3.8.3-7build1_arm64.deb ... 251s Unpacking python3-matplotlib (3.8.3-7build1) ... 251s Selecting previously unselected package python3-pytz. 251s Preparing to unpack .../081-python3-pytz_2025.1-3_all.deb ... 251s Unpacking python3-pytz (2025.1-3) ... 251s Selecting previously unselected package python3-tz. 251s Preparing to unpack .../082-python3-tz_2025.1-3_all.deb ... 251s Unpacking python3-tz (2025.1-3) ... 251s Selecting previously unselected package python3-pandas-lib:arm64. 251s Preparing to unpack .../083-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 251s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 252s Selecting previously unselected package python3-pandas. 252s Preparing to unpack .../084-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 252s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 252s Selecting previously unselected package cython3. 252s Preparing to unpack .../085-cython3_3.0.11+dfsg-2ubuntu2_arm64.deb ... 252s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 252s Selecting previously unselected package python3-joblib. 252s Preparing to unpack .../086-python3-joblib_1.4.2-3_all.deb ... 252s Unpacking python3-joblib (1.4.2-3) ... 252s Selecting previously unselected package python3-networkx. 252s Preparing to unpack .../087-python3-networkx_3.2.1-4ubuntu1_all.deb ... 252s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 253s Selecting previously unselected package 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255s Preparing to unpack .../115-cnvkit_0.9.12-1_all.deb ... 255s Unpacking cnvkit (0.9.12-1) ... 256s Selecting previously unselected package libgpgmepp6t64:arm64. 256s Preparing to unpack .../116-libgpgmepp6t64_1.24.2-1ubuntu2_arm64.deb ... 256s Unpacking libgpgmepp6t64:arm64 (1.24.2-1ubuntu2) ... 256s Selecting previously unselected package libpoppler147:arm64. 256s Preparing to unpack .../117-libpoppler147_25.03.0-2_arm64.deb ... 256s Unpacking libpoppler147:arm64 (25.03.0-2) ... 256s Selecting previously unselected package poppler-utils. 256s Preparing to unpack .../118-poppler-utils_25.03.0-2_arm64.deb ... 256s Unpacking poppler-utils (25.03.0-2) ... 256s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 256s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 256s Setting up liblcms2-2:arm64 (2.16-2) ... 256s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 256s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 256s Setting up libgpgmepp6t64:arm64 (1.24.2-1ubuntu2) ... 256s Setting up 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(2.1-6.1ubuntu2) ... 259s Setting up python3-platformdirs (4.3.6-1) ... 259s Setting up python3-tz (2025.1-3) ... 259s Setting up python3-fs (2.4.16-7) ... 259s Setting up unicode-data (15.1.0-1) ... 259s Setting up python3-decorator (5.1.1-5) ... 259s Setting up zip (3.0-14ubuntu2) ... 259s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 259s Setting up libblas3:arm64 (3.12.1-2) ... 259s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 259s Setting up python3-packaging (24.2-1) ... 259s Setting up python3-brotli (1.1.0-2build4) ... 259s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 259s Setting up python3-cycler (0.12.1-1) ... 259s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 259s Setting up fonts-dejavu-mono (2.37-8) ... 259s Setting up python3-kiwisolver (1.4.7-3build1) ... 260s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 260s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 260s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 260s Setting up fonts-dejavu-core (2.37-8) ... 260s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 260s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 260s Setting up libwebp7:arm64 (1.5.0-0.1) ... 260s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 260s Setting up libhts3t64:arm64 (1.21+ds-1) ... 260s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 260s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 260s Setting up libthai-data (0.1.29-2build1) ... 260s Setting up python3-dateutil (2.9.0-3) ... 261s Setting up sgml-base (1.31) ... 261s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 261s Setting up libpaper2:arm64 (2.2.5-0.3) ... 261s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 261s Setting up python3-mpmath (1.3.0-1) ... 261s Setting up python-matplotlib-data (3.8.3-7build1) ... 261s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 261s Setting up xdg-utils (1.2.1-2ubuntu1) ... 261s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 261s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 261s Setting up python3-pyfaidx (0.8.1.3-1) ... 261s Setting up python3-sympy (1.13.3-5) ... 268s Setting up libice6:arm64 (2:1.1.1-1) ... 268s Setting up liblapack3:arm64 (3.12.1-2) ... 268s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 268s Setting up python3-pysam (0.23.0+ds-1build1) ... 268s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 269s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 269s Setting up libpaper-utils (2.2.5-0.3) ... 269s Setting up xfonts-utils (1:7.7+7) ... 269s Setting up libthai0:arm64 (0.1.29-2build1) ... 269s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 269s Setting up libraqm0:arm64 (0.10.2-1) ... 269s Setting up python3-numpy (1:2.2.3+ds-5) ... 271s Setting up python3-lxml:arm64 (5.3.1-1build1) ... 271s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 271s Setting up xml-core (0.19) ... 271s Setting up python3-contourpy (1.3.1-1build1) ... 271s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 271s Setting up libsm6:arm64 (2:1.2.4-1) ... 271s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 271s Setting up fontconfig (2.15.0-2ubuntu1) ... 274s Regenerating fonts cache... done. 274s Setting up libxft2:arm64 (2.3.6-1build1) ... 274s Setting up python3-scipy (1.14.1-4ubuntu2) ... 277s Setting up libpoppler147:arm64 (25.03.0-2) ... 277s Setting up python3-pomegranate (0.15.0-1build1) ... 277s Setting up libtk8.6:arm64 (8.6.16-1) ... 277s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 277s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 277s Setting up python3.12-tk (3.12.9-1) ... 277s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 277s Setting up fonts-urw-base35 (20200910-8) ... 278s Setting up libcairo2:arm64 (1.18.2-2) ... 278s Setting up python3.13-tk (3.13.2-2) ... 278s Setting up python3-pil:arm64 (11.1.0-5build1) ... 278s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 283s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 283s Setting up python3-sklearn (1.4.2+dfsg-8) ... 285s Setting up poppler-utils (25.03.0-2) ... 285s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 285s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 286s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 286s Setting up python3-cairo (1.26.1-2build2) ... 286s Setting up blt (2.5.3+dfsg-8) ... 286s Setting up python3-tk:arm64 (3.13.1-1) ... 286s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 286s Setting up python3-rlpycairo (0.3.0-3) ... 286s Setting up r-base-core (4.4.3-1) ... 286s Creating config file /etc/R/Renviron with new version 286s Setting up python3-reportlab (4.3.1-1) ... 287s Setting up r-bioc-biocgenerics (0.52.0-2) ... 287s Setting up r-bioc-dnacopy (1.80.0-2) ... 287s Setting up python3-fonttools (4.55.3-2build1) ... 288s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 288s Setting up python3-matplotlib (3.8.3-7build1) ... 290s Processing triggers for libc-bin (2.41-1ubuntu1) ... 290s Processing triggers for man-db (2.13.0-1) ... 291s Processing triggers for install-info (7.1.1-1) ... 291s Processing triggers for sgml-base (1.31) ... 291s Setting up w3c-sgml-lib (1.3-3) ... 320s Setting up python3-biopython (1.85+dfsg-2build1) ... 321s Setting up cnvkit (0.9.12-1) ... 323s autopkgtest [01:32:22]: test run-unit-test: [----------------------- 324s cnvkit.py batch -n -f formats/chrM-Y-trunc.hg19.fa -m wgs formats/na12878-chrM-Y-trunc.bam -d build 327s CNVkit 0.9.12 327s WGS protocol: recommend '--annotate' option (e.g. refFlat.txt) to help locate genes in output files. 327s chrM: Scanning for accessible regions 327s Accessible region chrM:0-121 (size 121) 327s Accessible region chrM:122-1271 (size 1149) 327s Accessible region chrM:1274-1288 (size 14) 327s Accessible region chrM:1289-1547 (size 258) 327s Accessible region chrM:1553-16571 (size 15018) 327s chrY: Scanning for accessible regions 327s Accessible region chrY:500-14900 (size 14400) 327s Accessible region chrY:15600-22966 (size 7366) 327s chrY: Joining over small gaps 327s Joining chrY 500-14900 and 15600-22966 (gap size 700) 327s Wrote chrM-Y-trunc.hg19.bed with 1 regions 327s Detected file format: bed 327s Splitting large targets 327s Created directory build 327s Wrote build/chrM-Y-trunc.hg19.target.bed with 4 regions 327s Wrote build/chrM-Y-trunc.hg19.antitarget.bed with 0 regions 327s Building a flat reference... 327s Detected file format: bed 327s Calculating GC and RepeatMasker content in formats/chrM-Y-trunc.hg19.fa ... 327s Extracting sequences from chromosome chrY 327s Wrote build/reference.cnn with 4 regions 327s Running 1 samples in serial 327s Running the CNVkit pipeline on formats/na12878-chrM-Y-trunc.bam ... 327s Indexing BAM file formats/na12878-chrM-Y-trunc.bam 327s Processing reads in na12878-chrM-Y-trunc.bam 327s Time: 0.009 seconds (3960 reads/sec, 428 bins/sec) 327s Summary: #bins=4, #reads=37, mean=9.2500, min=0.0, max=21.0 327s Percent reads in regions: 0.063 (of 58636 mapped) 327s Wrote build/na12878-chrM-Y-trunc.targetcoverage.cnn with 4 regions 327s Skip processing na12878-chrM-Y-trunc.bam with empty regions file build/chrM-Y-trunc.hg19.antitarget.bed 327s Wrote build/na12878-chrM-Y-trunc.antitargetcoverage.cnn with 0 regions 327s Processing target: na12878-chrM-Y-trunc 327s Keeping 4 of 4 bins 327s Correcting for GC bias... 327s Processing antitarget: na12878-chrM-Y-trunc 327s Wrote build/na12878-chrM-Y-trunc.cnr with 4 regions 327s Segmenting build/na12878-chrM-Y-trunc.cnr ... 327s Segmenting with method 'cbs', significance threshold 1e-06, in 1 processes 327s Post-processing build/na12878-chrM-Y-trunc.cns ... 327s Wrote build/na12878-chrM-Y-trunc.cns with 1 regions 327s Applying filter 'ci' 327s Filtered by 'ci' from 1 to 1 rows 327s Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 327s Wrote build/na12878-chrM-Y-trunc.call.cns with 1 regions 327s Significant hits in 4/4 bins (100%) 327s Wrote build/na12878-chrM-Y-trunc.bintest.cns with 4 regions 328s 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/ 329s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 330s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 330s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 330s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 330s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 330s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 330s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 330s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 330s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 330s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 332s Number of target and antitarget files: 3, 3 332s No FASTA reference genome provided; skipping GC, RM calculations 332s Sample sex not provided; inferring from samples. 332s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 332s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 332s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 332s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 332s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 333s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 333s Loading build/p2-20_5.targetcoverage.cnn 333s Correcting for GC bias for p2-20_5... 333s Correcting for density bias for p2-20_5... 333s Loading build/p2-5_5.targetcoverage.cnn 333s Correcting for GC bias for p2-5_5... 333s Correcting for density bias for p2-5_5... 333s Loading build/p2-9_5.targetcoverage.cnn 333s Correcting for GC bias for p2-9_5... 333s Correcting for density bias for p2-9_5... 333s Loading build/p2-20_5.antitargetcoverage.cnn 333s Correcting for GC bias for p2-20_5... 333s Loading build/p2-5_5.antitargetcoverage.cnn 333s Correcting for GC bias for p2-5_5... 333s Loading build/p2-9_5.antitargetcoverage.cnn 333s Correcting for GC bias for p2-9_5... 333s Calculating average bin coverages 339s Calculating bin spreads 340s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 340s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 340s " chr1:2435319-2436685 log2=-0.709 spread=0.503 340s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 340s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 340s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 340s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 340s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 340s " chr1:120611883-120612051 log2=0.070 spread=0.050 340s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 340s " chr1:156842391-156842479 log2=-0.398 spread=0.290 340s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 340s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 340s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 340s " chr1:183481886-183481951 log2=-0.040 spread=0.119 340s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 340s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 340s " chr1:243800859-243801066 log2=0.023 spread=0.063 340s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 340s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 340s " chr2:25536716-25536891 log2=0.702 spread=0.033 340s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 340s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 340s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 340s REL chr2:61108881-61109061 log2=1.026 spread=0.559 340s " chr2:61128072-61128256 log2=0.115 spread=0.173 340s " chr2:61145275-61145462 log2=0.014 spread=0.099 340s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 340s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 340s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 340s " chr2:128095237-128095425 log2=0.215 spread=0.212 340s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 340s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 340s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 340s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 341s " chr3:97160189-97160367 log2=-0.050 spread=0.191 341s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 341s " chr3:142286854-142287031 log2=-0.076 spread=0.116 341s GAK chr4:896278-896357 log2=-1.505 spread=1.261 341s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 341s " chr4:1803044-1803507 log2=-0.073 spread=0.117 341s " chr4:1808792-1809022 log2=0.252 spread=0.108 341s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 341s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 341s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 341s " chr4:178514600-178514725 log2=-0.098 spread=0.096 341s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 341s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 341s " chr5:1295312-1295381 log2=-0.690 spread=0.462 341s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 341s " chr5:25519857-25520034 log2=-0.015 spread=0.095 341s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 341s " chr5:38962338-38962525 log2=0.005 spread=0.019 341s " chr5:38966685-38966862 log2=0.006 spread=0.165 341s " chr5:38978620-38978763 log2=0.040 spread=0.030 341s " chr5:39074133-39074327 log2=-0.158 spread=0.139 341s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 341s " chr5:51030131-51030313 log2=-0.034 spread=0.192 341s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 341s " chr5:56168412-56168590 log2=0.479 spread=0.038 341s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 341s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 341s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 341s " chr5:86637023-86637168 log2=0.054 spread=0.111 341s " chr5:86642414-86642592 log2=0.254 spread=0.162 341s " chr5:86648912-86649096 log2=0.092 spread=0.062 341s " chr5:86670598-86670778 log2=0.222 spread=0.198 341s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 341s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 341s APC chr5:112101965-112102138 log2=0.104 spread=0.217 341s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 341s " chr5:170837567-170837631 log2=0.085 spread=0.349 341s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 341s " chr5:180046203-180046404 log2=-1.531 spread=0.722 341s " chr5:180076418-180076603 log2=-2.224 spread=1.416 341s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 341s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 341s " chr6:31939599-31940313 log2=-19.582 spread=0.181 341s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 341s " chr6:31946632-31946824 log2=-20.052 spread=0.088 341s " chr6:31947142-31947366 log2=-20.114 spread=0.066 341s " chr6:31948176-31948360 log2=-19.982 spread=0.149 341s " chr6:31948382-31948612 log2=-19.757 spread=0.165 341s " chr6:31948730-31949253 log2=-20.048 spread=0.014 341s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 341s " chr6:32164046-32164227 log2=-19.755 spread=0.189 341s " chr6:32164652-32164888 log2=-19.984 spread=0.154 341s " chr6:32165021-32165403 log2=-19.625 spread=0.196 341s " chr6:32166163-32166545 log2=-20.043 spread=0.072 341s " chr6:32166648-32166962 log2=-3.514 spread=5.742 341s " chr6:32168554-32168821 log2=-19.601 spread=0.197 341s " chr6:32168844-32169306 log2=-19.683 spread=0.166 341s " chr6:32169801-32170391 log2=-19.405 spread=0.205 341s " chr6:32171492-32171691 log2=-20.095 spread=0.101 341s " chr6:32171861-32172198 log2=-3.141 spread=7.288 341s " chr6:32178478-32178749 log2=-19.927 spread=0.164 341s " chr6:32180197-32180441 log2=-10.902 spread=9.532 341s " chr6:32180544-32180722 log2=-19.675 spread=0.186 341s " chr6:32180857-32181062 log2=-19.562 spread=0.227 341s " chr6:32181411-32181646 log2=-19.966 spread=0.171 341s " chr6:32181832-32182066 log2=-19.961 spread=0.172 341s " chr6:32182948-32183194 log2=-19.935 spread=0.168 341s " chr6:32184667-32185079 log2=-19.923 spread=0.165 341s " chr6:32185720-32185919 log2=-19.707 spread=0.197 341s " chr6:32187317-32187601 log2=-19.765 spread=0.173 341s " chr6:32187871-32188094 log2=-19.660 spread=0.188 341s " chr6:32188127-32188451 log2=-19.622 spread=0.169 341s " chr6:32188481-32188693 log2=-19.902 spread=0.132 341s " chr6:32188704-32189133 log2=-19.501 spread=0.193 341s " chr6:32190258-32190616 log2=-19.570 spread=0.209 341s " chr6:32190724-32190908 log2=-19.540 spread=0.232 341s " chr6:32191570-32191668 log2=-19.773 spread=0.178 341s " chr6:32191676-32191753 log2=-19.374 spread=0.201 341s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 341s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 341s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 341s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 341s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 341s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 341s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 341s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 341s " chr6:128316545-128316699 log2=-0.070 spread=0.050 341s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 341s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 341s " chr6:157099442-157099991 log2=-0.846 spread=0.504 341s " chr6:157100042-157100634 log2=-1.570 spread=0.825 341s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 341s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 341s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 341s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 341s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 341s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 341s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 341s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 341s " chr7:98491365-98491541 log2=0.209 spread=0.153 341s " chr7:98493314-98493496 log2=0.389 spread=0.207 341s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 341s " chr7:128829048-128829358 log2=-0.474 spread=0.315 341s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 341s " chr7:140484736-140484912 log2=0.081 spread=0.150 341s " chr7:140487956-140488430 log2=-0.089 spread=0.142 341s " chr7:140493336-140493442 log2=-0.340 spread=0.283 341s " chr7:140624315-140624540 log2=-0.497 spread=0.342 341s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 341s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 341s " chr8:30941153-30941335 log2=0.079 spread=0.294 341s " chr8:30942625-30942802 log2=0.044 spread=0.247 341s " chr8:30947918-30948092 log2=0.151 spread=0.124 341s " chr8:31000128-31000252 log2=-0.099 spread=0.098 341s " chr8:31001006-31001182 log2=-0.002 spread=0.062 341s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 341s " chr8:37698557-37699898 log2=-0.612 spread=0.029 341s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 341s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 341s " chr8:48845528-48845758 log2=0.056 spread=0.196 341s " chr8:48866846-48867043 log2=-0.067 spread=0.097 341s " chr8:48868369-48868526 log2=-0.239 spread=0.174 341s " chr8:48872485-48872722 log2=-0.636 spread=0.464 341s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 341s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 341s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 341s " chr9:2101491-2101640 log2=0.244 spread=0.104 341s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 341s " chr9:5067014-5067883 log2=0.146 spread=0.089 341s " chr9:5068184-5070306 log2=0.133 spread=0.092 341s " chr9:5076944-5077152 log2=0.046 spread=0.137 341s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 341s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 341s " chr9:21986759-21986899 log2=0.058 spread=0.175 341s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 341s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 341s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 341s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 341s " chr9:87425375-87425452 log2=0.494 spread=0.066 341s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 341s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 341s " chr9:139250747-139251032 log2=-0.223 spread=0.273 341s " chr9:139252418-139252703 log2=-0.512 spread=0.264 341s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 341s " chr9:139417262-139417677 log2=-0.173 spread=0.191 341s " chr9:139440110-139440287 log2=-1.257 spread=0.500 341s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 341s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 341s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 341s " chr10:43600360-43600677 log2=-0.341 spread=0.222 341s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 341s " chr10:89685254-89685374 log2=0.244 spread=0.259 341s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 341s " chr10:93579008-93579121 log2=0.166 spread=0.220 341s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 341s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 341s " chr10:112679716-112679934 log2=-0.008 spread=0.028 341s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 341s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 341s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 341s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 341s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 341s " chr11:94170270-94170454 log2=0.095 spread=0.285 341s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 341s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 341s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 341s " chr11:108164020-108164234 log2=-0.056 spread=0.040 341s " chr11:108217986-108218135 log2=0.359 spread=0.277 341s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 341s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 341s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 341s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 341s " chr12:25391004-25391186 log2=0.368 spread=0.128 341s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 341s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 341s " chr12:51206782-51207287 log2=-0.012 spread=0.101 341s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 341s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 341s " chr13:26970356-26970536 log2=0.137 spread=0.121 341s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 341s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 341s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 341s " chr13:32903506-32903689 log2=0.019 spread=0.232 341s " chr13:32918645-32918823 log2=0.158 spread=0.114 341s " chr13:32920899-32921077 log2=0.014 spread=0.247 341s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 341s " chr13:48919164-48919369 log2=0.025 spread=0.094 341s " chr13:48921877-48922044 log2=0.106 spread=0.147 341s " chr13:48923026-48923204 log2=0.360 spread=0.016 341s " chr13:48938965-48939147 log2=0.084 spread=0.356 341s " chr13:48941578-48941767 log2=0.238 spread=0.212 341s " chr13:48947486-48947665 log2=0.025 spread=0.126 341s " chr13:48954166-48954251 log2=0.061 spread=0.273 341s " chr13:49037815-49038005 log2=0.063 spread=0.062 341s " chr13:49047410-49047589 log2=0.053 spread=0.170 341s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 341s " chr13:85527771-85527948 log2=0.007 spread=0.222 341s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 341s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 341s " chr13:110438332-110438432 log2=-3.643 spread=2.325 341s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 341s " chr14:20291466-20291612 log2=0.697 spread=0.248 341s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 341s " chr14:36989195-36989373 log2=0.023 spread=0.162 341s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 341s " chr14:50619741-50619923 log2=0.003 spread=0.272 341s " chr14:50697856-50698044 log2=0.277 spread=0.334 341s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 341s " chr14:71275790-71275923 log2=-2.815 spread=1.938 341s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 341s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 341s " chr15:38544477-38545455 log2=-0.348 spread=0.179 341s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 341s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 341s " chr15:41803968-41804185 log2=-2.202 spread=0.188 341s " chr15:41804261-41804494 log2=-0.402 spread=0.392 341s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 341s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 341s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 341s " chr16:2611404-2611585 log2=-5.171 spread=1.963 341s " chr16:2611721-2611943 log2=-11.810 spread=9.172 341s " chr16:2615504-2615725 log2=-20.113 spread=0.007 341s " chr16:2616307-2616486 log2=-20.054 spread=0.072 341s " chr16:2631267-2631414 log2=-20.009 spread=0.061 341s " chr16:2631583-2631734 log2=-20.089 spread=0.090 341s " chr16:2633363-2633616 log2=-20.101 spread=0.089 341s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 341s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 341s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 341s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 341s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 341s " chr16:50826460-50826650 log2=0.239 spread=0.204 341s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 341s " chr16:60005694-60005857 log2=-0.366 spread=0.298 341s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 341s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 341s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 341s " chr17:12011053-12011253 log2=0.028 spread=0.232 341s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 341s " chr17:29496854-29497046 log2=0.226 spread=0.193 341s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 341s " chr17:30519172-30519355 log2=0.163 spread=0.289 341s " chr17:30525911-30526093 log2=-0.157 spread=0.046 341s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 341s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 341s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 341s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 341s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 341s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 341s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 341s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 341s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 341s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 341s " chr19:2210351-2210545 log2=-0.860 spread=0.261 341s " chr19:2226130-2227152 log2=-0.113 spread=0.120 341s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 341s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 341s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 341s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 341s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 341s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 341s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 341s " chr19:15311544-15311749 log2=-1.887 spread=1.202 341s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 341s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 341s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 341s " chr19:33792774-33793010 log2=-1.781 spread=0.127 341s " chr19:33793014-33793356 log2=-0.541 spread=0.385 341s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 341s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 341s " chr19:45873698-45873881 log2=-0.522 spread=0.327 341s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 341s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 341s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 341s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 341s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 341s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 341s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 341s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 341s " chr21:36265140-36265318 log2=0.042 spread=0.039 341s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 341s " chr22:29115325-29115465 log2=0.055 spread=0.390 341s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 341s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 341s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 341s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 341s " chrX:1317372-1317594 log2=-21.121 spread=0.049 341s " chrX:1321225-1321435 log2=-20.851 spread=0.196 341s " chrX:1325274-1325530 log2=-21.121 spread=0.011 341s " chrX:1327651-1327830 log2=-21.000 spread=0.029 341s " chrX:1331391-1331576 log2=-21.018 spread=0.052 341s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 341s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 341s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 341s " chrX:123185143-123185290 log2=-1.018 spread=0.062 341s " chrX:123202378-123202544 log2=-0.959 spread=0.103 341s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 341s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 341s " chrY:9008607-9008759 log2=-1.012 spread=0.097 341s " chrY:13131970-13132039 log2=-1.004 spread=0.074 341s " chrY:19506485-19506650 log2=-1.018 spread=0.034 341s " chrY:21033918-21034071 log2=-1.013 spread=0.057 341s " chrY:28463435-28463622 log2=-0.952 spread=0.039 341s " chrY:28514033-28514208 log2=-0.992 spread=0.026 341s Antitargets: 108 (0.8597%) bins failed filters 341s Wrote build/reference-picard.cnn with 19209 regions 341s 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 343s Processing target: p2-5_5 343s Keeping 6308 of 6646 bins 343s Correcting for GC bias... 343s Correcting for density bias... 343s Processing antitarget: p2-5_5 343s Keeping 12455 of 12563 bins 343s Correcting for GC bias... 343s WARNING: Skipping correction for RepeatMasker bias 343s Targets are 1.18 x more variable than antitargets 344s Wrote build/p2-5_5.cnr with 18763 regions 344s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 346s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 346s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 346s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 348s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 349s 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 350s Processing target: p2-9_2 350s Keeping 6308 of 6646 bins 350s Correcting for GC bias... 350s Correcting for density bias... 351s Processing antitarget: p2-9_2 351s Keeping 12455 of 12563 bins 351s Correcting for GC bias... 351s WARNING: Skipping correction for RepeatMasker bias 351s Targets are 1.72 x more variable than antitargets 351s Wrote build/p2-9_2.cnr with 18763 regions 352s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 353s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 353s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 354s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 356s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 356s 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 358s Processing target: p2-20_1 358s Keeping 6308 of 6646 bins 358s Correcting for GC bias... 358s Correcting for density bias... 358s Processing antitarget: p2-20_1 358s Keeping 12455 of 12563 bins 359s Correcting for GC bias... 359s WARNING: Skipping correction for RepeatMasker bias 359s Targets are 1.12 x more variable than antitargets 359s Wrote build/p2-20_1.cnr with 18763 regions 359s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 361s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 361s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 362s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 364s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 364s 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 366s Processing target: p2-20_2 366s Keeping 6308 of 6646 bins 366s Correcting for GC bias... 366s Correcting for density bias... 366s Processing antitarget: p2-20_2 366s Keeping 12455 of 12563 bins 366s Correcting for GC bias... 366s WARNING: Skipping correction for RepeatMasker bias 366s Targets are 1.10 x more variable than antitargets 367s Wrote build/p2-20_2.cnr with 18763 regions 367s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 369s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 369s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 370s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 372s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 372s 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 374s Processing target: p2-20_3 374s Keeping 6308 of 6646 bins 374s Correcting for GC bias... 374s Correcting for density bias... 374s Processing antitarget: p2-20_3 374s Keeping 12455 of 12563 bins 374s Correcting for GC bias... 374s WARNING: Skipping correction for RepeatMasker bias 375s Antitargets are 1.09 x more variable than targets 375s Wrote build/p2-20_3.cnr with 18763 regions 375s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 377s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 377s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 378s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 379s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 380s 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 382s Processing target: p2-20_4 382s Keeping 6308 of 6646 bins 382s Correcting for GC bias... 382s Correcting for density bias... 382s Processing antitarget: p2-20_4 382s Keeping 12455 of 12563 bins 382s Correcting for GC bias... 382s WARNING: Skipping correction for RepeatMasker bias 382s Targets are 1.43 x more variable than antitargets 382s Wrote build/p2-20_4.cnr with 18763 regions 383s 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 384s Processing target: p2-20_5 385s Keeping 6308 of 6646 bins 385s Correcting for GC bias... 385s Correcting for density bias... 385s Processing antitarget: p2-20_5 385s Keeping 12455 of 12563 bins 385s Correcting for GC bias... 385s WARNING: Skipping correction for RepeatMasker bias 385s Targets are 2.50 x more variable than antitargets 385s Wrote build/p2-20_5.cnr with 18763 regions 386s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 387s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 394s Dropped 8 / 49 bins on chromosome chrY 395s Wrote build/p2-5_5.cns with 71 regions 395s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 397s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 398s Dropped 1 / 949 bins on chromosome chr6 404s Dropped 27 / 49 bins on chromosome chrY 404s Wrote build/p2-9_2.cns with 103 regions 405s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 406s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 414s Dropped 6 / 49 bins on chromosome chrY 414s Wrote build/p2-20_1.cns with 121 regions 415s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 416s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 424s Dropped 7 / 49 bins on chromosome chrY 424s Wrote build/p2-20_2.cns with 117 regions 425s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 426s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 433s Dropped 11 / 49 bins on chromosome chrY 434s Wrote build/p2-20_3.cns with 64 regions 434s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 436s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 444s Dropped 8 / 49 bins on chromosome chrY 444s Wrote build/p2-20_4.cns with 143 regions 445s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 447s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 453s Smoothing overshot at 1 / 123 indices: (-0.30060035404086427, 0.3250888018519485) vs. original (-0.363302, 0.311218) 454s Dropped 6 / 49 bins on chromosome chrY 454s Wrote build/p2-20_5.cns with 120 regions 455s 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 458s Wrote p2-5_5-scatter.pdf 458s 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 460s Smoothing overshot at 3 / 97 indices: (-19.900105868621704, -3.3099069223720528) vs. original (-19.294, -0.16431) 461s Wrote p2-9_2-scatter.pdf 462s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 464s Showing 1480 probes and 0 selected genes in region chr1 464s Wrote p2-9_2-chr1-scatter.pdf 464s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 466s Showing 201 probes and 0 selected genes in region chr21 466s Wrote p2-9_2-chr21-scatter.pdf 467s 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 469s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 469s Wrote p2-9_2-chr9p-scatter.pdf 469s 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 471s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 471s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 472s 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 474s Detected file format: bed 474s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 474s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 474s 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 474s /usr/bin/pdfunite 474s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 476s Treating sample p2-5_5 as female 485s Wrote p2-5_5-diagram.pdf 485s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 487s Treating sample p2-9_2 as female 495s Wrote p2-9_2-diagram.pdf 495s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 497s Treating sample p2-20_1 as female 505s Wrote p2-20_1-diagram.pdf 506s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 507s Treating sample p2-20_2 as female 515s Wrote p2-20_2-diagram.pdf 516s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 517s Treating sample p2-5_5 as female 517s Wrote p2-5_5-cbs-diagram.pdf 518s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 519s Treating sample p2-9_2 as female 520s Wrote p2-9_2-cbs-diagram.pdf 520s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 522s Treating sample p2-20_1 as female 522s Wrote p2-20_1-cbs-diagram.pdf 522s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 524s Treating sample p2-20_2 as female 524s Wrote p2-20_2-cbs-diagram.pdf 524s 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 526s Treating sample p2-5_5 as female 531s Wrote p2-5_5-both-diagram.pdf 531s 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 533s Treating sample p2-9_2 as female 539s Wrote p2-9_2-both-diagram.pdf 539s 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 541s Treating sample p2-20_1 as female 547s Wrote p2-20_1-both-diagram.pdf 547s 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 549s Treating sample p2-20_2 as female 554s Wrote p2-20_2-both-diagram.pdf 555s 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 555s /usr/bin/pdfunite 555s 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 557s Treating sample p2-5_5 as female 557s Treating sample p2-9_2 as female 557s Treating sample p2-20_1 as female 557s Treating sample p2-20_2 as female 557s Treating sample p2-20_3 as female 557s Treating sample p2-20_4 as female 557s Treating sample p2-20_5 as female 559s Wrote heatmap-picard.pdf 559s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 561s Found 14 gene breakpoints 561s Wrote p2-9_2-breaks.txt 561s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 563s Treating sample p2-9_2 as female 565s Found 323 gene-level gains and losses 565s Wrote p2-9_2-genemetrics.txt 565s 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 567s Wrote gender-picard.txt 567s 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 572s Wrote p2-all.cdt 572s 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 577s Wrote p2-all-jtv.txt 577s 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 579s Wrote p2-all.seg 579s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 581s Wrote p2-9_2.nexus 582s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 584s Selected test sample NA12882 and control sample NA12878 584s Loaded 3654 records; skipped: 514 somatic, 394 depth 584s Kept 2631 heterozygous of 3654 VCF records 586s Placed 705 variants into 18763 bins 586s Wrote p2-9_2.nexus-ogt 587s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 588s Treating sample p2-5_5 as female 588s Rescaling sample with purity 0.65, ploidy 2 588s Wrote build/p2-5_5.call.cns with 71 regions 589s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 591s Treating sample p2-9_2 as female 591s Rescaling sample with purity 0.65, ploidy 2 591s Wrote build/p2-9_2.call.cns with 103 regions 591s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 593s Treating sample p2-20_1 as female 593s Rescaling sample with purity 0.65, ploidy 2 593s Wrote build/p2-20_1.call.cns with 121 regions 593s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 595s Treating sample p2-20_2 as female 595s Rescaling sample with purity 0.65, ploidy 2 595s Wrote build/p2-20_2.call.cns with 117 regions 595s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 597s Treating sample p2-20_3 as female 597s Rescaling sample with purity 0.65, ploidy 2 597s Wrote build/p2-20_3.call.cns with 64 regions 597s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 599s Treating sample p2-20_4 as female 599s Rescaling sample with purity 0.65, ploidy 2 599s Wrote build/p2-20_4.call.cns with 143 regions 600s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 601s Treating sample p2-20_5 as female 601s Rescaling sample with purity 0.65, ploidy 2 601s Wrote build/p2-20_5.call.cns with 120 regions 602s 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 603s Treating sample p2-5_5.call as female 603s Treating sample p2-9_2.call as female 603s Treating sample p2-20_1.call as female 603s Treating sample p2-20_2.call as female 604s Treating sample p2-20_3.call as female 604s Treating sample p2-20_4.call as female 604s Treating sample p2-20_5.call as female 604s Wrote p2-all.bed 604s 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 606s Treating sample p2-9_2.call as female 606s Wrote p2-9_2.vcf 606s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 608s Wrote p2-9_2.theta2.input 609s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 609s --mean --median --mode --t-test \ 609s --stdev --mad --mse --iqr --bivar \ 609s --ci --pi --sem --smooth-bootstrap 611s Wrote p2-9_2-segmetrics.cns with 103 regions 612s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 612s --ci -b 50 -a 0.5 614s Wrote p2-5_5-segmetrics.cns with 71 regions 614s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 616s Wrote p2-5_5-metrics.tsv 616s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 618s Wrote p2-9_2-metrics.tsv 618s 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 621s Wrote p2-20-metrics.tsv 621s PASS 622s autopkgtest [01:37:21]: test run-unit-test: -----------------------] 622s run-unit-test PASS 622s autopkgtest [01:37:21]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 623s autopkgtest [01:37:22]: test pybuild-autopkgtest: preparing testbed 716s autopkgtest [01:38:55]: testbed dpkg architecture: arm64 716s autopkgtest [01:38:55]: testbed apt version: 2.9.33 716s autopkgtest [01:38:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 716s autopkgtest [01:38:55]: testbed release detected to be: plucky 717s autopkgtest [01:38:56]: updating testbed package index (apt update) 718s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 718s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 718s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 718s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 718s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 718s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 718s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 718s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [72.2 kB] 718s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1816 B] 718s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 718s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [316 kB] 718s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [13.9 kB] 718s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [16.8 kB] 718s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 719s Fetched 972 kB in 1s (1100 kB/s) 719s Reading package lists... 720s Reading package lists... 721s Building dependency tree... 721s Reading state information... 721s Calculating upgrade... 722s Calculating upgrade... 723s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 723s Reading package lists... 723s Building dependency tree... 723s Reading state information... 724s Solving dependencies... 724s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 724s autopkgtest [01:39:03]: upgrading testbed (apt dist-upgrade and autopurge) 724s Reading package lists... 725s Building dependency tree... 725s Reading state information... 726s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 726s Starting 2 pkgProblemResolver with broken count: 0 726s Done 727s Entering ResolveByKeep 727s 727s Calculating upgrade... 728s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 728s Reading package lists... 728s Building dependency tree... 728s Reading state information... 729s Starting pkgProblemResolver with broken count: 0 729s Starting 2 pkgProblemResolver with broken count: 0 729s Done 729s Solving dependencies... 729s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 733s Reading package lists... 733s Building dependency tree... 733s Reading state information... 733s Starting pkgProblemResolver with broken count: 0 733s Starting 2 pkgProblemResolver with broken count: 0 733s Done 734s The following NEW packages will be installed: 734s autoconf automake autopoint autotools-dev blt build-essential cnvkit cpp 734s cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper 734s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz fontconfig 734s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 734s fonts-urw-base35 g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu 734s gcc gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext 734s intltool-debian libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 734s libdatrie1 libdebhelper-perl libdeflate0 libfile-stripnondeterminism-perl 734s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 734s libgpgmepp6t64 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 734s libhwasan0 libice6 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 734s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 734s liblerc4 liblsan0 libmpc3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 734s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpoppler147 734s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 734s libthai-data libthai0 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 734s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 734s libxslt1.1 libxss1 libxt6t64 m4 po-debconf poppler-utils 734s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python-matplotlib-data 734s python3-all python3-biopython python3-brotli python3-build python3-cairo 734s python3-contourpy python3-cycler python3-dateutil python3-decorator 734s python3-fonttools python3-freetype python3-fs python3-importlib-metadata 734s python3-iniconfig python3-installer python3-joblib python3-kiwisolver 734s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-networkx 734s python3-numpy python3-numpy-dev python3-packaging python3-pandas 734s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 734s python3-pluggy python3-pomegranate python3-pyfaidx python3-pyproject-hooks 734s python3-pysam python3-pytest python3-pytz python3-reportlab 734s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 734s python3-sympy python3-threadpoolctl python3-tk python3-toml python3-tz 734s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-tk 734s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 734s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 734s xfonts-encodings xfonts-utils xml-core zip 734s 0 upgraded, 172 newly installed, 0 to remove and 0 not upgraded. 734s Need to get 239 MB of archives. 734s After this operation, 951 MB of additional disk space will be used. 734s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 735s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 735s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 735s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 735s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 735s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 735s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-7 [244 kB] 735s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3ubuntu1 [383 kB] 735s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 735s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.17-3ubuntu1 [572 kB] 735s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.23.1-1 [619 kB] 735s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 735s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 735s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 735s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 735s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 735s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 736s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 736s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 736s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 736s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 736s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 736s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 736s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 736s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 736s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-8 [624 kB] 736s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-8 [4824 B] 736s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 736s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 736s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 737s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 737s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 737s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 737s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 737s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 737s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 737s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 737s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 737s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 737s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 737s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 737s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 737s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 738s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 738s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 738s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 738s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 738s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 738s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 738s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 738s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 738s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 738s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.9-1 [115 kB] 738s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.2-2 [106 kB] 739s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tk arm64 3.13.1-1 [9770 B] 739s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 11.1.0-5build1 [9892 B] 739s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 739s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 739s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 739s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 739s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 739s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 739s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 739s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 739s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 739s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 739s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 739s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 739s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 739s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 739s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 739s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 739s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 739s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 739s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 739s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 739s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 739s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build2 [122 kB] 739s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 739s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 739s Get:81 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 739s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 739s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 739s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 739s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 739s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 739s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.3-1 [171 kB] 739s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 739s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 739s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.1-1build1 [182 kB] 739s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 739s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build4 [342 kB] 739s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 739s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-7 [90.8 kB] 739s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu2 [168 kB] 739s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.1-1build1 [1258 kB] 739s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.4.0+dfsg-1build1 [27.1 kB] 739s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 739s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 739s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.14.1-4ubuntu2 [16.7 MB] 740s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 740s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-5 [4229 kB] 747s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 747s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build3 [360 kB] 748s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.13.2-2 [886 B] 748s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 753s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.55.3-2build1 [1466 kB] 754s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-3build1 [50.7 kB] 754s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.2-1 [51.5 kB] 754s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 754s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-7build1 [17.3 MB] 760s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pytz all 2025.1-3 [162 kB] 760s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2025.1-3 [1866 B] 760s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-8build1 [4586 kB] 760s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 760s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 cython3 arm64 3.0.11+dfsg-2ubuntu2 [2436 kB] 761s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.4.2-3 [205 kB] 761s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 762s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pomegranate arm64 0.15.0-1build1 [3013 kB] 762s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 762s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 762s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 762s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 763s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.23.0+ds-1build1 [3621 kB] 763s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 763s Get:126 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-8 [4109 kB] 763s Get:127 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 764s Get:128 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 764s Get:129 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 764s Get:130 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 764s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 764s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 764s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 764s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 764s Get:135 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 764s Get:136 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 764s Get:137 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 764s Get:138 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 764s Get:139 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 764s Get:140 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 764s Get:141 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 764s Get:142 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 764s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 766s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 766s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-dnacopy arm64 1.80.0-2 [497 kB] 766s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 cnvkit all 0.9.12-1 [20.6 MB] 768s Get:147 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 768s Get:148 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.5.4-4 [168 kB] 768s Get:149 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 768s Get:150 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 768s Get:151 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 768s Get:152 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 768s Get:153 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-2 [46.1 kB] 768s Get:154 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 768s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.23.1-1 [998 kB] 768s Get:156 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 768s Get:157 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 768s Get:158 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.24.1ubuntu2 [895 kB] 768s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20250308 [118 kB] 768s Get:160 http://ftpmaster.internal/ubuntu plucky/main arm64 libgpgmepp6t64 arm64 1.24.2-1ubuntu2 [119 kB] 768s Get:161 http://ftpmaster.internal/ubuntu plucky/main arm64 libpoppler147 arm64 25.03.0-2 [1154 kB] 768s Get:162 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-utils arm64 25.03.0-2 [212 kB] 768s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20250308 [1744 B] 768s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 768s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 768s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.45.1-1 [57.7 kB] 768s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 768s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 768s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20250308 [1726 B] 768s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 768s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 768s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.5-1 [252 kB] 769s Preconfiguring packages ... 769s Fetched 239 MB in 34s (7078 kB/s) 769s Selecting previously unselected package python3-numpy-dev:arm64. 769s (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 ... 81647 files and directories currently installed.) 769s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 769s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 769s Selecting previously unselected package libblas3:arm64. 769s Preparing to unpack .../001-libblas3_3.12.1-2_arm64.deb ... 769s Unpacking libblas3:arm64 (3.12.1-2) ... 769s Selecting previously unselected package libgfortran5:arm64. 769s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 769s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 769s Selecting previously unselected package liblapack3:arm64. 769s Preparing to unpack .../003-liblapack3_3.12.1-2_arm64.deb ... 769s Unpacking liblapack3:arm64 (3.12.1-2) ... 769s Selecting previously unselected package python3-numpy. 769s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 769s Unpacking python3-numpy (1:2.2.3+ds-5) ... 770s Selecting previously unselected package sgml-base. 770s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 770s Unpacking sgml-base (1.31) ... 770s Selecting previously unselected package m4. 770s Preparing to unpack .../006-m4_1.4.19-7_arm64.deb ... 770s Unpacking m4 (1.4.19-7) ... 770s Selecting previously unselected package autoconf. 770s Preparing to unpack .../007-autoconf_2.72-3ubuntu1_all.deb ... 770s Unpacking autoconf (2.72-3ubuntu1) ... 770s Selecting previously unselected package autotools-dev. 770s Preparing to unpack .../008-autotools-dev_20220109.1_all.deb ... 770s Unpacking autotools-dev (20220109.1) ... 770s Selecting previously unselected package automake. 770s Preparing to unpack .../009-automake_1%3a1.17-3ubuntu1_all.deb ... 770s Unpacking automake (1:1.17-3ubuntu1) ... 770s Selecting previously unselected package autopoint. 770s Preparing to unpack .../010-autopoint_0.23.1-1_all.deb ... 770s Unpacking autopoint (0.23.1-1) ... 770s Selecting previously unselected package libtcl8.6:arm64. 770s Preparing to unpack .../011-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 770s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 770s Selecting previously unselected package fonts-dejavu-mono. 770s Preparing to unpack .../012-fonts-dejavu-mono_2.37-8_all.deb ... 770s Unpacking fonts-dejavu-mono (2.37-8) ... 771s Selecting previously unselected package fonts-dejavu-core. 771s Preparing to unpack .../013-fonts-dejavu-core_2.37-8_all.deb ... 771s Unpacking fonts-dejavu-core (2.37-8) ... 771s Selecting previously unselected package libfontenc1:arm64. 771s Preparing to unpack .../014-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 771s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 771s Selecting previously unselected package x11-common. 771s Preparing to unpack .../015-x11-common_1%3a7.7+23ubuntu3_all.deb ... 771s Unpacking x11-common (1:7.7+23ubuntu3) ... 771s Selecting previously unselected package xfonts-encodings. 771s Preparing to unpack .../016-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 771s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 771s Selecting previously unselected package xfonts-utils. 771s Preparing to unpack .../017-xfonts-utils_1%3a7.7+7_arm64.deb ... 771s Unpacking xfonts-utils (1:7.7+7) ... 771s Selecting previously unselected package fonts-urw-base35. 771s Preparing to unpack .../018-fonts-urw-base35_20200910-8_all.deb ... 771s Unpacking fonts-urw-base35 (20200910-8) ... 771s Selecting previously unselected package fontconfig-config. 771s Preparing to unpack .../019-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 772s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 772s Selecting previously unselected package libfontconfig1:arm64. 772s Preparing to unpack .../020-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 772s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 772s Selecting previously unselected package libxrender1:arm64. 772s Preparing to unpack .../021-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 772s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 772s Selecting previously unselected package libxft2:arm64. 772s Preparing to unpack .../022-libxft2_2.3.6-1build1_arm64.deb ... 772s Unpacking libxft2:arm64 (2.3.6-1build1) ... 772s Selecting previously unselected package libxss1:arm64. 772s Preparing to unpack .../023-libxss1_1%3a1.2.3-1build3_arm64.deb ... 772s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 772s Selecting previously unselected package libtk8.6:arm64. 772s Preparing to unpack .../024-libtk8.6_8.6.16-1_arm64.deb ... 772s Unpacking libtk8.6:arm64 (8.6.16-1) ... 772s Selecting previously unselected package tk8.6-blt2.5. 772s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-8_arm64.deb ... 772s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 772s Selecting previously unselected package blt. 772s Preparing to unpack .../026-blt_2.5.3+dfsg-8_arm64.deb ... 772s Unpacking blt (2.5.3+dfsg-8) ... 772s Selecting previously unselected package libisl23:arm64. 772s Preparing to unpack .../027-libisl23_0.27-1_arm64.deb ... 772s Unpacking libisl23:arm64 (0.27-1) ... 772s Selecting previously unselected package libmpc3:arm64. 772s Preparing to unpack .../028-libmpc3_1.3.1-1build2_arm64.deb ... 772s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 772s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 772s Preparing to unpack .../029-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 772s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 772s Selecting previously unselected package cpp-14. 772s Preparing to unpack .../030-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 772s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 772s Selecting previously unselected package cpp-aarch64-linux-gnu. 772s Preparing to unpack .../031-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 772s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 772s Selecting previously unselected package cpp. 773s Preparing to unpack .../032-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 773s Unpacking cpp (4:14.2.0-1ubuntu1) ... 773s Selecting previously unselected package libcc1-0:arm64. 773s Preparing to unpack .../033-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libgomp1:arm64. 773s Preparing to unpack .../034-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libitm1:arm64. 773s Preparing to unpack .../035-libitm1_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libasan8:arm64. 773s Preparing to unpack .../036-libasan8_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package liblsan0:arm64. 773s Preparing to unpack .../037-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libtsan2:arm64. 773s Preparing to unpack .../038-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libubsan1:arm64. 773s Preparing to unpack .../039-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libhwasan0:arm64. 773s Preparing to unpack .../040-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 773s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 773s Selecting previously unselected package libgcc-14-dev:arm64. 773s Preparing to unpack .../041-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 773s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 773s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 773s Preparing to unpack .../042-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 773s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 774s Selecting previously unselected package gcc-14. 774s Preparing to unpack .../043-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 774s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 774s Selecting previously unselected package gcc-aarch64-linux-gnu. 774s Preparing to unpack .../044-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 774s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 774s Selecting previously unselected package gcc. 774s Preparing to unpack .../045-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 774s Unpacking gcc (4:14.2.0-1ubuntu1) ... 774s Selecting previously unselected package libstdc++-14-dev:arm64. 774s Preparing to unpack .../046-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 774s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 774s Selecting previously unselected package g++-14-aarch64-linux-gnu. 774s Preparing to unpack .../047-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 774s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 775s Selecting previously unselected package g++-14. 775s Preparing to unpack .../048-g++-14_14.2.0-17ubuntu3_arm64.deb ... 775s Unpacking g++-14 (14.2.0-17ubuntu3) ... 775s Selecting previously unselected package g++-aarch64-linux-gnu. 775s Preparing to unpack .../049-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 775s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 775s Selecting previously unselected package g++. 775s Preparing to unpack .../050-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 775s Unpacking g++ (4:14.2.0-1ubuntu1) ... 775s Selecting previously unselected package build-essential. 775s Preparing to unpack .../051-build-essential_12.10ubuntu1_arm64.deb ... 775s Unpacking build-essential (12.10ubuntu1) ... 775s Selecting previously unselected package python3.12-tk. 775s Preparing to unpack .../052-python3.12-tk_3.12.9-1_arm64.deb ... 775s Unpacking python3.12-tk (3.12.9-1) ... 775s Selecting previously unselected package python3.13-tk. 775s Preparing to unpack .../053-python3.13-tk_3.13.2-2_arm64.deb ... 775s Unpacking python3.13-tk (3.13.2-2) ... 775s Selecting previously unselected package python3-tk:arm64. 775s Preparing to unpack .../054-python3-tk_3.13.1-1_arm64.deb ... 775s Unpacking python3-tk:arm64 (3.13.1-1) ... 775s Selecting previously unselected package python3-pil.imagetk:arm64. 775s Preparing to unpack .../055-python3-pil.imagetk_11.1.0-5build1_arm64.deb ... 775s Unpacking python3-pil.imagetk:arm64 (11.1.0-5build1) ... 775s Selecting previously unselected package libimagequant0:arm64. 775s Preparing to unpack .../056-libimagequant0_2.18.0-1build1_arm64.deb ... 775s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 775s Selecting previously unselected package libjpeg-turbo8:arm64. 775s Preparing to unpack .../057-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 775s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 775s Selecting previously unselected package libjpeg8:arm64. 775s Preparing to unpack .../058-libjpeg8_8c-2ubuntu11_arm64.deb ... 775s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 775s Selecting previously unselected package liblcms2-2:arm64. 775s Preparing to unpack .../059-liblcms2-2_2.16-2_arm64.deb ... 775s Unpacking liblcms2-2:arm64 (2.16-2) ... 775s Selecting previously unselected package libopenjp2-7:arm64. 775s Preparing to unpack .../060-libopenjp2-7_2.5.3-2_arm64.deb ... 775s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 776s Selecting previously unselected package libgraphite2-3:arm64. 776s Preparing to unpack .../061-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 776s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 776s Selecting previously unselected package libharfbuzz0b:arm64. 776s Preparing to unpack .../062-libharfbuzz0b_10.2.0-1_arm64.deb ... 776s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 776s Selecting previously unselected package libraqm0:arm64. 776s Preparing to unpack .../063-libraqm0_0.10.2-1_arm64.deb ... 776s Unpacking libraqm0:arm64 (0.10.2-1) ... 776s Selecting previously unselected package libdeflate0:arm64. 776s Preparing to unpack .../064-libdeflate0_1.23-1_arm64.deb ... 776s Unpacking libdeflate0:arm64 (1.23-1) ... 776s Selecting previously unselected package libjbig0:arm64. 776s Preparing to unpack .../065-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 776s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 776s Selecting previously unselected package liblerc4:arm64. 776s Preparing to unpack .../066-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 776s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 776s Selecting previously unselected package libsharpyuv0:arm64. 776s Preparing to unpack .../067-libsharpyuv0_1.5.0-0.1_arm64.deb ... 776s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 776s Selecting previously unselected package libwebp7:arm64. 776s Preparing to unpack .../068-libwebp7_1.5.0-0.1_arm64.deb ... 776s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 776s Selecting previously unselected package libtiff6:arm64. 776s Preparing to unpack .../069-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 776s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 776s Selecting previously unselected package libwebpdemux2:arm64. 776s Preparing to unpack .../070-libwebpdemux2_1.5.0-0.1_arm64.deb ... 776s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 776s Selecting previously unselected package libwebpmux3:arm64. 776s Preparing to unpack .../071-libwebpmux3_1.5.0-0.1_arm64.deb ... 776s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 776s Selecting previously unselected package python3-pil:arm64. 776s Preparing to unpack .../072-python3-pil_11.1.0-5build1_arm64.deb ... 776s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 776s Selecting previously unselected package libpixman-1-0:arm64. 776s Preparing to unpack .../073-libpixman-1-0_0.44.0-3_arm64.deb ... 776s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 776s Selecting previously unselected package libxcb-render0:arm64. 776s Preparing to unpack .../074-libxcb-render0_1.17.0-2_arm64.deb ... 776s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 776s Selecting previously unselected package libxcb-shm0:arm64. 776s Preparing to unpack .../075-libxcb-shm0_1.17.0-2_arm64.deb ... 776s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 776s Selecting previously unselected package libcairo2:arm64. 776s Preparing to unpack .../076-libcairo2_1.18.2-2_arm64.deb ... 776s Unpacking libcairo2:arm64 (1.18.2-2) ... 776s Selecting previously unselected package python3-cairo. 777s Preparing to unpack .../077-python3-cairo_1.26.1-2build2_arm64.deb ... 777s Unpacking python3-cairo (1.26.1-2build2) ... 777s Selecting previously unselected package python3-freetype. 777s Preparing to unpack .../078-python3-freetype_2.5.1-1_all.deb ... 777s Unpacking python3-freetype (2.5.1-1) ... 777s Selecting previously unselected package python3-rlpycairo. 777s Preparing to unpack .../079-python3-rlpycairo_0.3.0-3_all.deb ... 777s Unpacking python3-rlpycairo (0.3.0-3) ... 777s Selecting previously unselected package python3-reportlab. 777s Preparing to unpack .../080-python3-reportlab_4.3.1-1_all.deb ... 777s Unpacking python3-reportlab (4.3.1-1) ... 777s Selecting previously unselected package xml-core. 777s Preparing to unpack .../081-xml-core_0.19_all.deb ... 777s Unpacking xml-core (0.19) ... 777s Selecting previously unselected package w3c-sgml-lib. 777s Preparing to unpack .../082-w3c-sgml-lib_1.3-3_all.deb ... 777s Unpacking w3c-sgml-lib (1.3-3) ... 777s Selecting previously unselected package python3-biopython. 777s Preparing to unpack .../083-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 777s Unpacking python3-biopython (1.85+dfsg-2build1) ... 777s Selecting previously unselected package libjs-jquery. 777s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 777s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 777s Selecting previously unselected package libjs-jquery-ui. 777s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 777s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 777s Selecting previously unselected package fonts-lyx. 777s Preparing to unpack .../086-fonts-lyx_2.4.3-1_all.deb ... 777s Unpacking fonts-lyx (2.4.3-1) ... 777s Selecting previously unselected package python-matplotlib-data. 777s Preparing to unpack .../087-python-matplotlib-data_3.8.3-7build1_all.deb ... 777s Unpacking python-matplotlib-data (3.8.3-7build1) ... 778s Selecting previously unselected package python3-dateutil. 778s Preparing to unpack .../088-python3-dateutil_2.9.0-3_all.deb ... 778s Unpacking python3-dateutil (2.9.0-3) ... 778s Selecting previously unselected package python3-contourpy. 778s Preparing to unpack .../089-python3-contourpy_1.3.1-1build1_arm64.deb ... 778s Unpacking python3-contourpy (1.3.1-1build1) ... 778s Selecting previously unselected package python3-cycler. 778s Preparing to unpack .../090-python3-cycler_0.12.1-1_all.deb ... 778s Unpacking python3-cycler (0.12.1-1) ... 778s Selecting previously unselected package python3-brotli. 778s Preparing to unpack .../091-python3-brotli_1.1.0-2build4_arm64.deb ... 778s Unpacking python3-brotli (1.1.0-2build4) ... 778s Selecting previously unselected package python3-platformdirs. 778s Preparing to unpack .../092-python3-platformdirs_4.3.6-1_all.deb ... 778s Unpacking python3-platformdirs (4.3.6-1) ... 778s Selecting previously unselected package python3-fs. 778s Preparing to unpack .../093-python3-fs_2.4.16-7_all.deb ... 778s Unpacking python3-fs (2.4.16-7) ... 778s Selecting previously unselected package libxslt1.1:arm64. 778s Preparing to unpack .../094-libxslt1.1_1.1.39-0exp1ubuntu2_arm64.deb ... 778s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 778s Selecting previously unselected package python3-lxml:arm64. 778s Preparing to unpack .../095-python3-lxml_5.3.1-1build1_arm64.deb ... 778s Unpacking python3-lxml:arm64 (5.3.1-1build1) ... 778s Selecting previously unselected package python3-lz4. 778s Preparing to unpack .../096-python3-lz4_4.4.0+dfsg-1build1_arm64.deb ... 778s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 778s Selecting previously unselected package python3-decorator. 778s Preparing to unpack .../097-python3-decorator_5.1.1-5_all.deb ... 778s Unpacking python3-decorator (5.1.1-5) ... 778s Selecting previously unselected package liblbfgsb0:arm64. 778s Preparing to unpack .../098-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 778s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 778s Selecting previously unselected package python3-scipy. 778s Preparing to unpack .../099-python3-scipy_1.14.1-4ubuntu2_arm64.deb ... 778s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 779s Selecting previously unselected package python3-mpmath. 779s Preparing to unpack .../100-python3-mpmath_1.3.0-1_all.deb ... 779s Unpacking python3-mpmath (1.3.0-1) ... 779s Selecting previously unselected package python3-sympy. 779s Preparing to unpack .../101-python3-sympy_1.13.3-5_all.deb ... 779s Unpacking python3-sympy (1.13.3-5) ... 779s Selecting previously unselected package python3-ufolib2. 779s Preparing to unpack .../102-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 779s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 780s Selecting previously unselected package python3-unicodedata2. 780s Preparing to unpack .../103-python3-unicodedata2_15.1.0+ds-1build3_arm64.deb ... 780s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 780s Selecting previously unselected package python3-all. 780s Preparing to unpack .../104-python3-all_3.13.2-2_arm64.deb ... 780s Unpacking python3-all (3.13.2-2) ... 780s Selecting previously unselected package unicode-data. 780s Preparing to unpack .../105-unicode-data_15.1.0-1_all.deb ... 780s Unpacking unicode-data (15.1.0-1) ... 780s Selecting previously unselected package python3-fonttools. 780s Preparing to unpack .../106-python3-fonttools_4.55.3-2build1_arm64.deb ... 780s Unpacking python3-fonttools (4.55.3-2build1) ... 780s Selecting previously unselected package python3-kiwisolver. 780s Preparing to unpack .../107-python3-kiwisolver_1.4.7-3build1_arm64.deb ... 780s Unpacking python3-kiwisolver (1.4.7-3build1) ... 780s Selecting previously unselected package python3-packaging. 780s Preparing to unpack .../108-python3-packaging_24.2-1_all.deb ... 780s Unpacking python3-packaging (24.2-1) ... 780s Selecting previously unselected package libqhull-r8.0:arm64. 780s Preparing to unpack .../109-libqhull-r8.0_2020.2-6build1_arm64.deb ... 780s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 780s Selecting previously unselected package python3-matplotlib. 780s Preparing to unpack .../110-python3-matplotlib_3.8.3-7build1_arm64.deb ... 780s Unpacking python3-matplotlib (3.8.3-7build1) ... 781s Selecting previously unselected package python3-pytz. 781s Preparing to unpack .../111-python3-pytz_2025.1-3_all.deb ... 781s Unpacking python3-pytz (2025.1-3) ... 781s Selecting previously unselected package python3-tz. 781s Preparing to unpack .../112-python3-tz_2025.1-3_all.deb ... 781s Unpacking python3-tz (2025.1-3) ... 781s Selecting previously unselected package python3-pandas-lib:arm64. 781s Preparing to unpack .../113-python3-pandas-lib_2.2.3+dfsg-8build1_arm64.deb ... 781s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 781s Selecting previously unselected package python3-pandas. 781s Preparing to unpack .../114-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 781s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 782s Selecting previously unselected package cython3. 782s Preparing to unpack .../115-cython3_3.0.11+dfsg-2ubuntu2_arm64.deb ... 782s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 782s Selecting previously unselected package python3-joblib. 782s Preparing to unpack .../116-python3-joblib_1.4.2-3_all.deb ... 782s Unpacking python3-joblib (1.4.2-3) ... 782s Selecting previously unselected package python3-networkx. 782s Preparing to unpack .../117-python3-networkx_3.2.1-4ubuntu1_all.deb ... 782s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 783s Selecting previously unselected package python3-pomegranate. 783s Preparing to unpack .../118-python3-pomegranate_0.15.0-1build1_arm64.deb ... 783s Unpacking python3-pomegranate (0.15.0-1build1) ... 783s Selecting previously unselected package python3-importlib-metadata. 783s Preparing to unpack .../119-python3-importlib-metadata_8.6.1-1_all.deb ... 783s Unpacking python3-importlib-metadata (8.6.1-1) ... 783s Selecting previously unselected package python3-pyfaidx. 783s Preparing to unpack .../120-python3-pyfaidx_0.8.1.3-1_all.deb ... 783s Unpacking python3-pyfaidx (0.8.1.3-1) ... 783s Selecting previously unselected package libhtscodecs2:arm64. 783s Preparing to unpack .../121-libhtscodecs2_1.6.1-2_arm64.deb ... 783s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 783s Selecting previously unselected package libhts3t64:arm64. 783s Preparing to unpack .../122-libhts3t64_1.21+ds-1_arm64.deb ... 783s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 783s Selecting previously unselected package python3-pysam. 783s Preparing to unpack .../123-python3-pysam_0.23.0+ds-1build1_arm64.deb ... 783s Unpacking python3-pysam (0.23.0+ds-1build1) ... 784s Selecting previously unselected package python3-threadpoolctl. 784s Preparing to unpack .../124-python3-threadpoolctl_3.1.0-1_all.deb ... 784s Unpacking python3-threadpoolctl (3.1.0-1) ... 784s Selecting previously unselected package python3-sklearn-lib:arm64. 784s Preparing to unpack .../125-python3-sklearn-lib_1.4.2+dfsg-8_arm64.deb ... 784s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 784s Selecting previously unselected package python3-sklearn. 784s Preparing to unpack .../126-python3-sklearn_1.4.2+dfsg-8_all.deb ... 784s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 784s Selecting previously unselected package zip. 784s Preparing to unpack .../127-zip_3.0-14ubuntu2_arm64.deb ... 784s Unpacking zip (3.0-14ubuntu2) ... 784s Selecting previously unselected package unzip. 784s Preparing to unpack .../128-unzip_6.0-28ubuntu6_arm64.deb ... 784s Unpacking unzip (6.0-28ubuntu6) ... 784s Selecting previously unselected package libpaper2:arm64. 784s Preparing to unpack .../129-libpaper2_2.2.5-0.3_arm64.deb ... 784s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 784s Selecting previously unselected package libpaper-utils. 785s Preparing to unpack .../130-libpaper-utils_2.2.5-0.3_arm64.deb ... 785s Unpacking libpaper-utils (2.2.5-0.3) ... 785s Selecting previously unselected package xdg-utils. 785s Preparing to unpack .../131-xdg-utils_1.2.1-2ubuntu1_all.deb ... 785s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 785s Selecting previously unselected package fontconfig. 785s Preparing to unpack .../132-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 785s Unpacking fontconfig (2.15.0-2ubuntu1) ... 785s Selecting previously unselected package libthai-data. 785s Preparing to unpack .../133-libthai-data_0.1.29-2build1_all.deb ... 785s Unpacking libthai-data (0.1.29-2build1) ... 785s Selecting previously unselected package libdatrie1:arm64. 785s Preparing to unpack .../134-libdatrie1_0.2.13-3build1_arm64.deb ... 785s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 785s Selecting previously unselected package libthai0:arm64. 785s Preparing to unpack .../135-libthai0_0.1.29-2build1_arm64.deb ... 785s Unpacking libthai0:arm64 (0.1.29-2build1) ... 785s Selecting previously unselected package libpango-1.0-0:arm64. 785s Preparing to unpack .../136-libpango-1.0-0_1.56.2-1_arm64.deb ... 785s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 785s Selecting previously unselected package libpangoft2-1.0-0:arm64. 785s Preparing to unpack .../137-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 785s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 785s Selecting previously unselected package libpangocairo-1.0-0:arm64. 785s Preparing to unpack .../138-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 785s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 785s Selecting previously unselected package libice6:arm64. 785s Preparing to unpack .../139-libice6_2%3a1.1.1-1_arm64.deb ... 785s Unpacking libice6:arm64 (2:1.1.1-1) ... 785s Selecting previously unselected package libsm6:arm64. 785s Preparing to unpack .../140-libsm6_2%3a1.2.4-1_arm64.deb ... 785s Unpacking libsm6:arm64 (2:1.2.4-1) ... 785s Selecting previously unselected package libxt6t64:arm64. 785s Preparing to unpack .../141-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 785s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 785s Selecting previously unselected package r-base-core. 785s Preparing to unpack .../142-r-base-core_4.4.3-1_arm64.deb ... 785s Unpacking r-base-core (4.4.3-1) ... 786s Selecting previously unselected package r-bioc-biocgenerics. 786s Preparing to unpack .../143-r-bioc-biocgenerics_0.52.0-2_all.deb ... 786s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 786s Selecting previously unselected package r-bioc-dnacopy. 786s Preparing to unpack .../144-r-bioc-dnacopy_1.80.0-2_arm64.deb ... 786s Unpacking r-bioc-dnacopy (1.80.0-2) ... 786s Selecting previously unselected package cnvkit. 786s Preparing to unpack .../145-cnvkit_0.9.12-1_all.deb ... 786s Unpacking cnvkit (0.9.12-1) ... 787s Selecting previously unselected package libdebhelper-perl. 787s Preparing to unpack .../146-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 787s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 787s Selecting previously unselected package libtool. 787s Preparing to unpack .../147-libtool_2.5.4-4_all.deb ... 787s Unpacking libtool (2.5.4-4) ... 787s Selecting previously unselected package dh-autoreconf. 787s Preparing to unpack .../148-dh-autoreconf_20_all.deb ... 787s Unpacking dh-autoreconf (20) ... 787s Selecting previously unselected package libarchive-zip-perl. 787s Preparing to unpack .../149-libarchive-zip-perl_1.68-1_all.deb ... 787s Unpacking libarchive-zip-perl (1.68-1) ... 787s Selecting previously unselected package libfile-stripnondeterminism-perl. 787s Preparing to unpack .../150-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 787s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 787s Selecting previously unselected package dh-strip-nondeterminism. 787s Preparing to unpack .../151-dh-strip-nondeterminism_1.14.1-2_all.deb ... 787s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 787s Selecting previously unselected package debugedit. 787s Preparing to unpack .../152-debugedit_1%3a5.1-2_arm64.deb ... 787s Unpacking debugedit (1:5.1-2) ... 787s Selecting previously unselected package dwz. 787s Preparing to unpack .../153-dwz_0.15-1build6_arm64.deb ... 787s Unpacking dwz (0.15-1build6) ... 787s Selecting previously unselected package gettext. 787s Preparing to unpack .../154-gettext_0.23.1-1_arm64.deb ... 787s Unpacking gettext (0.23.1-1) ... 787s Selecting previously unselected package intltool-debian. 787s Preparing to unpack .../155-intltool-debian_0.35.0+20060710.6_all.deb ... 787s Unpacking intltool-debian (0.35.0+20060710.6) ... 787s Selecting previously unselected package po-debconf. 787s Preparing to unpack .../156-po-debconf_1.0.21+nmu1_all.deb ... 787s Unpacking po-debconf (1.0.21+nmu1) ... 787s Selecting previously unselected package debhelper. 787s Preparing to unpack .../157-debhelper_13.24.1ubuntu2_all.deb ... 787s Unpacking debhelper (13.24.1ubuntu2) ... 787s Selecting previously unselected package dh-python. 787s Preparing to unpack .../158-dh-python_6.20250308_all.deb ... 787s Unpacking dh-python (6.20250308) ... 787s Selecting previously unselected package libgpgmepp6t64:arm64. 787s Preparing to unpack .../159-libgpgmepp6t64_1.24.2-1ubuntu2_arm64.deb ... 787s Unpacking libgpgmepp6t64:arm64 (1.24.2-1ubuntu2) ... 787s Selecting previously unselected package libpoppler147:arm64. 787s Preparing to unpack .../160-libpoppler147_25.03.0-2_arm64.deb ... 787s Unpacking libpoppler147:arm64 (25.03.0-2) ... 788s Selecting previously unselected package poppler-utils. 788s Preparing to unpack .../161-poppler-utils_25.03.0-2_arm64.deb ... 788s Unpacking poppler-utils (25.03.0-2) ... 788s Selecting previously unselected package pybuild-plugin-autopkgtest. 788s Preparing to unpack .../162-pybuild-plugin-autopkgtest_6.20250308_all.deb ... 788s Unpacking pybuild-plugin-autopkgtest (6.20250308) ... 788s Selecting previously unselected package python3-pyproject-hooks. 788s Preparing to unpack .../163-python3-pyproject-hooks_1.2.0-1_all.deb ... 788s Unpacking python3-pyproject-hooks (1.2.0-1) ... 788s Selecting previously unselected package python3-toml. 788s Preparing to unpack .../164-python3-toml_0.10.2-1_all.deb ... 788s Unpacking python3-toml (0.10.2-1) ... 788s Selecting previously unselected package python3-wheel. 788s Preparing to unpack .../165-python3-wheel_0.45.1-1_all.deb ... 788s Unpacking python3-wheel (0.45.1-1) ... 788s Selecting previously unselected package python3-build. 788s Preparing to unpack .../166-python3-build_1.2.2-1_all.deb ... 788s Unpacking python3-build (1.2.2-1) ... 788s Selecting previously unselected package python3-installer. 788s Preparing to unpack .../167-python3-installer_0.7.0+dfsg1-3_all.deb ... 788s Unpacking python3-installer (0.7.0+dfsg1-3) ... 788s Selecting previously unselected package pybuild-plugin-pyproject. 788s Preparing to unpack .../168-pybuild-plugin-pyproject_6.20250308_all.deb ... 788s Unpacking pybuild-plugin-pyproject (6.20250308) ... 788s Selecting previously unselected package python3-iniconfig. 788s Preparing to unpack .../169-python3-iniconfig_1.1.1-2_all.deb ... 788s Unpacking python3-iniconfig (1.1.1-2) ... 788s Selecting previously unselected package python3-pluggy. 788s Preparing to unpack .../170-python3-pluggy_1.5.0-1_all.deb ... 788s Unpacking python3-pluggy (1.5.0-1) ... 788s Selecting previously unselected package python3-pytest. 788s Preparing to unpack .../171-python3-pytest_8.3.5-1_all.deb ... 788s Unpacking python3-pytest (8.3.5-1) ... 788s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 788s Setting up dh-python (6.20250308) ... 788s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 788s Setting up liblcms2-2:arm64 (2.16-2) ... 788s Setting up python3-iniconfig (1.1.1-2) ... 789s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 789s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 789s Setting up libgpgmepp6t64:arm64 (1.24.2-1ubuntu2) ... 789s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 789s Setting up python3-importlib-metadata (8.6.1-1) ... 789s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 789s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 789s Setting up python3-joblib (1.4.2-3) ... 789s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 789s Setting up libxcb-render0:arm64 (1.17.0-2) ... 789s Setting up libarchive-zip-perl (1.68-1) ... 789s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 790s Setting up fonts-lyx (2.4.3-1) ... 790s Setting up unzip (6.0-28ubuntu6) ... 790s Setting up libdebhelper-perl (13.24.1ubuntu2) ... 790s Setting up python3-threadpoolctl (3.1.0-1) ... 790s Setting up x11-common (1:7.7+23ubuntu3) ... 790s Setting up libdeflate0:arm64 (1.23-1) ... 790s Setting up m4 (1.4.19-7) ... 790s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 790s Setting up python3-all (3.13.2-2) ... 790s Setting up python3-pytz (2025.1-3) ... 790s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 790s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 790s Setting up python3-freetype (2.5.1-1) ... 791s Setting up python3-networkx (3.2.1-4ubuntu1) ... 793s Setting up python3-wheel (0.45.1-1) ... 793s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 793s Setting up python3-platformdirs (4.3.6-1) ... 793s Setting up python3-tz (2025.1-3) ... 793s Setting up python3-fs (2.4.16-7) ... 793s Setting up unicode-data (15.1.0-1) ... 793s Setting up python3-decorator (5.1.1-5) ... 794s Setting up zip (3.0-14ubuntu2) ... 794s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 794s Setting up autotools-dev (20220109.1) ... 794s Setting up libblas3:arm64 (3.12.1-2) ... 794s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 794s Setting up python3-packaging (24.2-1) ... 794s Setting up python3-pyproject-hooks (1.2.0-1) ... 794s Setting up python3-brotli (1.1.0-2build4) ... 794s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 794s Setting up python3-cycler (0.12.1-1) ... 794s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 794s Setting up fonts-dejavu-mono (2.37-8) ... 794s Setting up python3-kiwisolver (1.4.7-3build1) ... 795s Setting up libmpc3:arm64 (1.3.1-1build2) ... 795s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 795s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 795s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 795s Setting up autopoint (0.23.1-1) ... 796s Setting up fonts-dejavu-core (2.37-8) ... 796s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 796s Setting up python3-toml (0.10.2-1) ... 796s Setting up python3-installer (0.7.0+dfsg1-3) ... 796s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 796s Setting up autoconf (2.72-3ubuntu1) ... 796s Setting up python3-pluggy (1.5.0-1) ... 796s Setting up libwebp7:arm64 (1.5.0-0.1) ... 796s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ... 796s Setting up dwz (0.15-1build6) ... 796s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ... 796s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ... 796s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu2) ... 796s Setting up debugedit (1:5.1-2) ... 796s Setting up libhts3t64:arm64 (1.21+ds-1) ... 796s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 796s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 796s Setting up libthai-data (0.1.29-2build1) ... 796s Setting up python3-dateutil (2.9.0-3) ... 796s Setting up sgml-base (1.31) ... 796s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 796s Setting up libpaper2:arm64 (2.2.5-0.3) ... 796s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ... 796s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 796s Setting up python3-mpmath (1.3.0-1) ... 797s Setting up libisl23:arm64 (0.27-1) ... 797s Setting up python3-build (1.2.2-1) ... 797s Setting up python-matplotlib-data (3.8.3-7build1) ... 797s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 797s Setting up xdg-utils (1.2.1-2ubuntu1) ... 797s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 797s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ... 797s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 797s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 797s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 797s Setting up automake (1:1.17-3ubuntu1) ... 797s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 797s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 797s Setting up python3-pyfaidx (0.8.1.3-1) ... 797s Setting up python3-sympy (1.13.3-5) ... 803s Setting up libice6:arm64 (2:1.1.1-1) ... 803s Setting up liblapack3:arm64 (3.12.1-2) ... 803s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 803s Setting up gettext (0.23.1-1) ... 803s Setting up python3-pysam (0.23.0+ds-1build1) ... 803s Setting up pybuild-plugin-pyproject (6.20250308) ... 803s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 804s Setting up python3-pytest (8.3.5-1) ... 804s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 804s Setting up libpaper-utils (2.2.5-0.3) ... 804s Setting up xfonts-utils (1:7.7+7) ... 804s Setting up intltool-debian (0.35.0+20060710.6) ... 804s Setting up libthai0:arm64 (0.1.29-2build1) ... 804s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 804s Setting up libraqm0:arm64 (0.10.2-1) ... 804s Setting up python3-numpy (1:2.2.3+ds-5) ... 806s Setting up dh-strip-nondeterminism (1.14.1-2) ... 806s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 806s Setting up python3-lxml:arm64 (5.3.1-1build1) ... 806s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 806s Setting up xml-core (0.19) ... 806s Setting up python3-contourpy (1.3.1-1build1) ... 806s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 806s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 806s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 806s Setting up libsm6:arm64 (2:1.2.4-1) ... 806s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 806s Setting up fontconfig (2.15.0-2ubuntu1) ... 809s Regenerating fonts cache... done. 809s Setting up libxft2:arm64 (2.3.6-1build1) ... 809s Setting up python3-scipy (1.14.1-4ubuntu2) ... 812s Setting up libpoppler147:arm64 (25.03.0-2) ... 812s Setting up po-debconf (1.0.21+nmu1) ... 812s Setting up python3-pomegranate (0.15.0-1build1) ... 812s Setting up libtk8.6:arm64 (8.6.16-1) ... 812s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-8build1) ... 812s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 812s Setting up python3.12-tk (3.12.9-1) ... 812s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ... 812s Setting up fonts-urw-base35 (20200910-8) ... 812s Setting up libcairo2:arm64 (1.18.2-2) ... 812s Setting up python3.13-tk (3.13.2-2) ... 812s Setting up python3-pil:arm64 (11.1.0-5build1) ... 813s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 813s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 818s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 818s Setting up python3-sklearn (1.4.2+dfsg-8) ... 819s Setting up cpp-14 (14.2.0-17ubuntu3) ... 819s Setting up cpp (4:14.2.0-1ubuntu1) ... 819s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 819s Setting up poppler-utils (25.03.0-2) ... 819s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 819s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 819s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 819s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 819s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 819s Setting up python3-cairo (1.26.1-2build2) ... 819s Setting up blt (2.5.3+dfsg-8) ... 819s Setting up python3-tk:arm64 (3.13.1-1) ... 820s Setting up gcc-14 (14.2.0-17ubuntu3) ... 820s Setting up python3-pil.imagetk:arm64 (11.1.0-5build1) ... 820s Setting up python3-rlpycairo (0.3.0-3) ... 820s Setting up r-base-core (4.4.3-1) ... 820s Creating config file /etc/R/Renviron with new version 820s Setting up python3-reportlab (4.3.1-1) ... 821s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 821s Setting up g++-14 (14.2.0-17ubuntu3) ... 821s Setting up r-bioc-biocgenerics (0.52.0-2) ... 821s Setting up libtool (2.5.4-4) ... 821s Setting up gcc (4:14.2.0-1ubuntu1) ... 821s Setting up dh-autoreconf (20) ... 821s Setting up g++ (4:14.2.0-1ubuntu1) ... 821s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 821s Setting up r-bioc-dnacopy (1.80.0-2) ... 821s Setting up build-essential (12.10ubuntu1) ... 821s Setting up debhelper (13.24.1ubuntu2) ... 821s Setting up pybuild-plugin-autopkgtest (6.20250308) ... 821s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 821s Setting up python3-fonttools (4.55.3-2build1) ... 822s Setting up python3-matplotlib (3.8.3-7build1) ... 823s Processing triggers for libc-bin (2.41-1ubuntu1) ... 823s Processing triggers for man-db (2.13.0-1) ... 825s Processing triggers for install-info (7.1.1-1) ... 825s Processing triggers for sgml-base (1.31) ... 825s Setting up w3c-sgml-lib (1.3-3) ... 851s Setting up python3-biopython (1.85+dfsg-2build1) ... 852s Setting up cnvkit (0.9.12-1) ... 859s autopkgtest [01:41:18]: test pybuild-autopkgtest: pybuild-autopkgtest 859s autopkgtest [01:41:18]: test pybuild-autopkgtest: [----------------------- 859s pybuild-autopkgtest 860s I: pybuild base:311: cd /tmp/autopkgtest.3T9x0w/autopkgtest_tmp/build; python3.13 -m pytest test 863s ============================= test session starts ============================== 863s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 863s rootdir: /tmp/autopkgtest.3T9x0w/autopkgtest_tmp/build 863s configfile: pyproject.toml 863s plugins: typeguard-4.4.2 863s collected 70 items 863s 869s test/test_cnvlib.py ........... [ 15%] 980s test/test_commands.py ............................. [ 57%] 985s test/test_genome.py ................... [ 84%] 986s test/test_io.py .......... [ 98%] 996s test/test_r.py . [100%] 996s 996s ======================== 70 passed in 136.00s (0:02:15) ======================== 997s autopkgtest [01:43:36]: test pybuild-autopkgtest: -----------------------] 998s autopkgtest [01:43:37]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 998s pybuild-autopkgtest PASS 998s autopkgtest [01:43:37]: @@@@@@@@@@@@@@@@@@@@ summary 998s run-unit-test PASS 998s pybuild-autopkgtest PASS 1016s nova [W] Using flock in prodstack6-arm64 1016s Creating nova instance adt-plucky-arm64-cnvkit-20250316-012658-juju-7f2275-prod-proposed-migration-environment-2-9f5d3358-6796-4d12-a882-bf9375edc1cd from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1016s nova [W] Timed out waiting for 5cdf3696-5b79-456f-a6b9-c3c12d78042d to get deleted. 1016s nova [W] Using flock in prodstack6-arm64 1016s Creating nova instance adt-plucky-arm64-cnvkit-20250316-012658-juju-7f2275-prod-proposed-migration-environment-2-9f5d3358-6796-4d12-a882-bf9375edc1cd from image adt/ubuntu-plucky-arm64-server-20250316.img (UUID 08b37ce2-d71b-4e08-a72e-06f281931f28)... 1016s nova [W] Timed out waiting for 753fb6ed-b6cd-4f52-aec0-73f3d2976c9d to get deleted.