0s autopkgtest [15:53:25]: starting date and time: 2025-10-18 15:53:25+0000 0s autopkgtest [15:53:25]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:53:25]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v8h68m54/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-3.secgroup --name adt-resolute-i386-cnvkit-20251018-155325-juju-7f2275-prod-proposed-migration-environment-20-e1262310-29d4-4b01-b022-253b9a6bfdfc --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-i386-cnvkit-20251018-155325-juju-7f2275-prod-proposed-migration-environment-20-e1262310-29d4-4b01-b022-253b9a6bfdfc from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 32s autopkgtest [15:53:57]: testbed dpkg architecture: amd64 33s autopkgtest [15:53:58]: testbed apt version: 3.1.6ubuntu2 33s autopkgtest [15:53:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [15:53:58]: testbed release detected to be: None 34s autopkgtest [15:53:59]: updating testbed package index (apt update) 34s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 34s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 34s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 34s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 34s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 34s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 34s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 34s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 34s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 34s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 34s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 34s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 34s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 34s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 34s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 34s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 34s Fetched 972 kB in 1s (1715 kB/s) 35s Reading package lists... 35s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 35s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 35s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 36s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 36s Reading package lists... 36s Reading package lists... 36s Building dependency tree... 36s Reading state information... 36s Calculating upgrade... 36s The following packages will be upgraded: 36s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 36s libpython3-stdlib python3 python3-minimal 36s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 36s Need to get 2751 kB of archives. 36s After this operation, 2048 B of additional disk space will be used. 36s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 36s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 36s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 36s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 37s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 37s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 37s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 37s dpkg-preconfigure: unable to re-open stdin: No such file or directory 37s Fetched 2751 kB in 0s (9547 kB/s) 37s (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 ... 78439 files and directories currently installed.) 37s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 37s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 37s Setting up python3-minimal (3.13.7-2) ... 37s (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 ... 78439 files and directories currently installed.) 37s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 37s running python pre-rtupdate hooks for python3.13... 37s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 37s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 37s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 37s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 37s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 37s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 37s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 37s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 37s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 37s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 37s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 37s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 37s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 37s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 37s Setting up apt (3.1.8ubuntu1) ... 38s Setting up python3 (3.13.7-2) ... 38s running python rtupdate hooks for python3.13... 38s running python post-rtupdate hooks for python3.13... 38s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 38s Processing triggers for man-db (2.13.1-1) ... 39s Processing triggers for libc-bin (2.42-0ubuntu3) ... 39s autopkgtest [15:54:04]: upgrading testbed (apt dist-upgrade and autopurge) 39s Reading package lists... 39s Building dependency tree... 39s Reading state information... 40s Calculating upgrade... 40s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 40s Reading package lists... 40s Building dependency tree... 40s Reading state information... 40s Solving dependencies... 40s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 40s autopkgtest [15:54:05]: rebooting testbed after setup commands that affected boot 54s autopkgtest [15:54:19]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 56s autopkgtest [15:54:21]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 59s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cnvkit 0.9.12-1 (dsc) [2483 B] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cnvkit 0.9.12-1 (tar) [32.1 MB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cnvkit 0.9.12-1 (diff) [20.8 kB] 59s gpgv: Signature made Thu Feb 6 14:25:04 2025 UTC 59s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 59s gpgv: issuer "crusoe@debian.org" 59s gpgv: Can't check signature: No public key 59s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.12-1.dsc: no acceptable signature found 59s autopkgtest [15:54:24]: testing package cnvkit version 0.9.12-1 60s autopkgtest [15:54:25]: build not needed 65s autopkgtest [15:54:30]: test run-unit-test: preparing testbed 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 65s Solving dependencies... 65s The following NEW packages will be installed: 65s blt cnvkit cython3 fontconfig fontconfig-config fonts-dejavu-core 65s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 65s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgpgme11t64 65s libgpgmepp6t64 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 65s libicu76 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery 65s libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 libnspr4 libnss3 libopenjp2-7 65s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 65s libpaper2 libpixman-1-0 libpoppler147 libqhull-r8.0 libraqm0 libsharpyuv0 65s libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libwebp7 65s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 65s libxslt1.1 libxss1 libxt6t64 libzopfli1 poppler-utils python-matplotlib-data 65s python3-biopython python3-brotli python3-cairo python3-charset-normalizer 65s python3-contourpy python3-cycler python3-dateutil python3-decorator 65s python3-fonttools python3-freetype python3-fs python3-joblib 65s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 65s python3-mpmath python3-networkx python3-numpy python3-numpy-dev 65s python3-packaging python3-pandas python3-pandas-lib python3-pil 65s python3-pil.imagetk python3-platformdirs python3-pomegranate python3-pyfaidx 65s python3-pysam python3-pytz python3-reportlab python3-rlpycairo python3-scipy 65s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 65s python3-tk python3-ufolib2 python3-unicodedata2 python3-zopfli python3.13-tk 65s r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base tk8.6-blt2.5 65s unicode-data unzip w3c-sgml-lib x11-common xdg-utils xfonts-encodings 65s xfonts-utils xml-core zip 65s 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. 65s Need to get 193 MB of archives. 65s After this operation, 800 MB of additional disk space will be used. 65s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 65s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 65s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 66s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 66s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 66s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 66s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 66s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 67s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 67s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 67s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 67s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 67s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 67s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 67s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 67s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 67s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 67s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 67s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 67s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 67s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 67s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.2-1 [129 kB] 67s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] 67s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.5-1 [9916 B] 67s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu1 [9700 B] 67s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 67s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 67s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 67s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 67s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 67s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 67s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 67s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 67s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 67s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 67s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 67s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 67s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 67s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 67s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 67s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 67s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 67s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu1 [496 kB] 67s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 67s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 67s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 67s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 67s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2 [124 kB] 67s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 67s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 67s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.2-1 [1145 kB] 67s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 67s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 67s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 67s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB] 67s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 67s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 67s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-1 [171 kB] 67s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 68s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 68s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 68s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 68s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build5 [342 kB] 68s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 68s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 68s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.1 [172 kB] 68s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.1-1 [1528 kB] 68s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.0+dfsg-2 [26.6 kB] 68s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 68s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1 [16.6 MB] 68s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 68s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 68s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 68s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 68s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 68s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.2.3.post1-1 [10.8 kB] 68s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 68s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-1 [1497 kB] 68s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 68s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 68s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 68s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.1+dfsg1-4 [18.0 MB] 69s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-3 [163 kB] 69s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4949 kB] 69s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 69s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 69s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 69s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 69s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 69s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyfaidx all 0.8.1.3-2 [29.7 kB] 69s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 69s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 69s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 69s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 69s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 69s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 69s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB] 69s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB] 69s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 69s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 69s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 69s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu76 amd64 76.1-4ubuntu2 [11.2 MB] 69s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 69s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 69s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.13-4 [19.3 kB] 69s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 69s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-1build1 [247 kB] 69s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1build1 [55.0 kB] 69s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1build1 [30.3 kB] 69s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 69s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 69s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 70s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.1-1 [28.9 MB] 70s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 70s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 70s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 70s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpgme11t64 amd64 1.24.2-3ubuntu1 [144 kB] 70s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpgmepp6t64 amd64 1.24.2-3ubuntu1 [124 kB] 70s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libnspr4 amd64 2:4.36-1ubuntu2 [118 kB] 70s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 libnss3 amd64 2:3.114-1 [1483 kB] 70s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libpoppler147 amd64 25.03.0-10 [1225 kB] 70s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 poppler-utils amd64 25.03.0-10 [229 kB] 71s Preconfiguring packages ... 71s Fetched 193 MB in 5s (36.8 MB/s) 71s Selecting previously unselected package python3-numpy-dev:amd64. 71s (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 ... 78439 files and directories currently installed.) 71s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 71s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 71s Selecting previously unselected package libblas3:amd64. 71s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ... 71s Unpacking libblas3:amd64 (3.12.1-6build1) ... 71s Selecting previously unselected package libgfortran5:amd64. 71s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 71s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 71s Selecting previously unselected package liblapack3:amd64. 71s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ... 71s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 71s Selecting previously unselected package python3-numpy. 71s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 71s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 71s Selecting previously unselected package libtcl8.6:amd64. 71s Preparing to unpack .../005-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 71s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 71s Selecting previously unselected package fonts-dejavu-mono. 71s Preparing to unpack .../006-fonts-dejavu-mono_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-mono (2.37-8) ... 71s Selecting previously unselected package fonts-dejavu-core. 71s Preparing to unpack .../007-fonts-dejavu-core_2.37-8_all.deb ... 71s Unpacking fonts-dejavu-core (2.37-8) ... 71s Selecting previously unselected package libfontenc1:amd64. 71s Preparing to unpack .../008-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 71s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 71s Selecting previously unselected package x11-common. 71s Preparing to unpack .../009-x11-common_1%3a7.7+24ubuntu1_all.deb ... 71s Unpacking x11-common (1:7.7+24ubuntu1) ... 71s Selecting previously unselected package xfonts-encodings. 71s Preparing to unpack .../010-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 71s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 71s Selecting previously unselected package xfonts-utils. 71s Preparing to unpack .../011-xfonts-utils_1%3a7.7+7_amd64.deb ... 71s Unpacking xfonts-utils (1:7.7+7) ... 71s Selecting previously unselected package fonts-urw-base35. 71s Preparing to unpack .../012-fonts-urw-base35_20200910-8_all.deb ... 71s Unpacking fonts-urw-base35 (20200910-8) ... 71s Selecting previously unselected package fontconfig-config. 71s Preparing to unpack .../013-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 71s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 71s Selecting previously unselected package libfontconfig1:amd64. 71s Preparing to unpack .../014-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 71s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 71s Selecting previously unselected package libxrender1:amd64. 71s Preparing to unpack .../015-libxrender1_1%3a0.9.12-1_amd64.deb ... 71s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 71s Selecting previously unselected package libxft2:amd64. 71s Preparing to unpack .../016-libxft2_2.3.6-1build1_amd64.deb ... 71s Unpacking libxft2:amd64 (2.3.6-1build1) ... 71s Selecting previously unselected package libxss1:amd64. 71s Preparing to unpack .../017-libxss1_1%3a1.2.3-1build3_amd64.deb ... 71s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 71s Selecting previously unselected package libtk8.6:amd64. 71s Preparing to unpack .../018-libtk8.6_8.6.17-1_amd64.deb ... 71s Unpacking libtk8.6:amd64 (8.6.17-1) ... 71s Selecting previously unselected package tk8.6-blt2.5. 71s Preparing to unpack .../019-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 71s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 71s Selecting previously unselected package blt. 71s Preparing to unpack .../020-blt_2.5.3+dfsg-8_amd64.deb ... 71s Unpacking blt (2.5.3+dfsg-8) ... 71s Selecting previously unselected package python3-charset-normalizer. 71s Preparing to unpack .../021-python3-charset-normalizer_3.4.2-1_amd64.deb ... 71s Unpacking python3-charset-normalizer (3.4.2-1) ... 71s Selecting previously unselected package python3.13-tk. 71s Preparing to unpack .../022-python3.13-tk_3.13.7-1_amd64.deb ... 71s Unpacking python3.13-tk (3.13.7-1) ... 71s Selecting previously unselected package python3-tk:amd64. 71s Preparing to unpack .../023-python3-tk_3.13.5-1_amd64.deb ... 71s Unpacking python3-tk:amd64 (3.13.5-1) ... 71s Selecting previously unselected package python3-pil.imagetk:amd64. 71s Preparing to unpack .../024-python3-pil.imagetk_11.3.0-1ubuntu1_amd64.deb ... 71s Unpacking python3-pil.imagetk:amd64 (11.3.0-1ubuntu1) ... 71s Selecting previously unselected package libgomp1:amd64. 71s Preparing to unpack .../025-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 71s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 71s Selecting previously unselected package libimagequant0:amd64. 71s Preparing to unpack .../026-libimagequant0_2.18.0-1build1_amd64.deb ... 71s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 71s Selecting previously unselected package libjpeg-turbo8:amd64. 71s Preparing to unpack .../027-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 71s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 71s Selecting previously unselected package libjpeg8:amd64. 71s Preparing to unpack .../028-libjpeg8_8c-2ubuntu11_amd64.deb ... 71s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 71s Selecting previously unselected package liblcms2-2:amd64. 71s Preparing to unpack .../029-liblcms2-2_2.16-2_amd64.deb ... 71s Unpacking liblcms2-2:amd64 (2.16-2) ... 71s Selecting previously unselected package libopenjp2-7:amd64. 71s Preparing to unpack .../030-libopenjp2-7_2.5.3-2.1_amd64.deb ... 71s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 71s Selecting previously unselected package libgraphite2-3:amd64. 71s Preparing to unpack .../031-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 71s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 71s Selecting previously unselected package libharfbuzz0b:amd64. 71s Preparing to unpack .../032-libharfbuzz0b_10.2.0-1_amd64.deb ... 71s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 71s Selecting previously unselected package libraqm0:amd64. 71s Preparing to unpack .../033-libraqm0_0.10.3-1_amd64.deb ... 71s Unpacking libraqm0:amd64 (0.10.3-1) ... 71s Selecting previously unselected package libdeflate0:amd64. 71s Preparing to unpack .../034-libdeflate0_1.23-2_amd64.deb ... 71s Unpacking libdeflate0:amd64 (1.23-2) ... 71s Selecting previously unselected package libjbig0:amd64. 71s Preparing to unpack .../035-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 71s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 71s Selecting previously unselected package liblerc4:amd64. 71s Preparing to unpack .../036-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 71s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 71s Selecting previously unselected package libsharpyuv0:amd64. 71s Preparing to unpack .../037-libsharpyuv0_1.5.0-0.1_amd64.deb ... 71s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 71s Selecting previously unselected package libwebp7:amd64. 71s Preparing to unpack .../038-libwebp7_1.5.0-0.1_amd64.deb ... 71s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 71s Selecting previously unselected package libtiff6:amd64. 71s Preparing to unpack .../039-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 71s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 71s Selecting previously unselected package libwebpdemux2:amd64. 71s Preparing to unpack .../040-libwebpdemux2_1.5.0-0.1_amd64.deb ... 71s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 71s Selecting previously unselected package libwebpmux3:amd64. 71s Preparing to unpack .../041-libwebpmux3_1.5.0-0.1_amd64.deb ... 71s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 71s Selecting previously unselected package python3-pil:amd64. 72s Preparing to unpack .../042-python3-pil_11.3.0-1ubuntu1_amd64.deb ... 72s Unpacking python3-pil:amd64 (11.3.0-1ubuntu1) ... 72s Selecting previously unselected package libpixman-1-0:amd64. 72s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_amd64.deb ... 72s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 72s Selecting previously unselected package libxcb-render0:amd64. 72s Preparing to unpack .../044-libxcb-render0_1.17.0-2build1_amd64.deb ... 72s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 72s Selecting previously unselected package libxcb-shm0:amd64. 72s Preparing to unpack .../045-libxcb-shm0_1.17.0-2build1_amd64.deb ... 72s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 72s Selecting previously unselected package libcairo2:amd64. 72s Preparing to unpack .../046-libcairo2_1.18.4-1build1_amd64.deb ... 72s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 72s Selecting previously unselected package python3-cairo. 72s Preparing to unpack .../047-python3-cairo_1.27.0-2_amd64.deb ... 72s Unpacking python3-cairo (1.27.0-2) ... 72s Selecting previously unselected package python3-freetype. 72s Preparing to unpack .../048-python3-freetype_2.5.1-1_all.deb ... 72s Unpacking python3-freetype (2.5.1-1) ... 72s Selecting previously unselected package python3-rlpycairo. 72s Preparing to unpack .../049-python3-rlpycairo_0.3.0-3_all.deb ... 72s Unpacking python3-rlpycairo (0.3.0-3) ... 72s Selecting previously unselected package python3-reportlab. 72s Preparing to unpack .../050-python3-reportlab_4.4.2-1_all.deb ... 72s Unpacking python3-reportlab (4.4.2-1) ... 72s Selecting previously unselected package sgml-base. 72s Preparing to unpack .../051-sgml-base_1.31+nmu1_all.deb ... 72s Unpacking sgml-base (1.31+nmu1) ... 72s Selecting previously unselected package xml-core. 72s Preparing to unpack .../052-xml-core_0.19_all.deb ... 72s Unpacking xml-core (0.19) ... 72s Selecting previously unselected package w3c-sgml-lib. 72s Preparing to unpack .../053-w3c-sgml-lib_1.3-3_all.deb ... 72s Unpacking w3c-sgml-lib (1.3-3) ... 72s Selecting previously unselected package python3-biopython. 72s Preparing to unpack .../054-python3-biopython_1.85+dfsg-4_amd64.deb ... 72s Unpacking python3-biopython (1.85+dfsg-4) ... 72s Selecting previously unselected package libjs-jquery. 72s Preparing to unpack .../055-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 72s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 72s Selecting previously unselected package libjs-jquery-ui. 72s Preparing to unpack .../056-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 72s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 72s Selecting previously unselected package fonts-lyx. 72s Preparing to unpack .../057-fonts-lyx_2.4.4-1_all.deb ... 72s Unpacking fonts-lyx (2.4.4-1) ... 72s Selecting previously unselected package python-matplotlib-data. 72s Preparing to unpack .../058-python-matplotlib-data_3.10.1+dfsg1-4_all.deb ... 72s Unpacking python-matplotlib-data (3.10.1+dfsg1-4) ... 72s Selecting previously unselected package python3-dateutil. 72s Preparing to unpack .../059-python3-dateutil_2.9.0-4_all.deb ... 72s Unpacking python3-dateutil (2.9.0-4) ... 72s Selecting previously unselected package python3-contourpy. 72s Preparing to unpack .../060-python3-contourpy_1.3.1-1build1_amd64.deb ... 72s Unpacking python3-contourpy (1.3.1-1build1) ... 72s Selecting previously unselected package python3-cycler. 72s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 72s Unpacking python3-cycler (0.12.1-1) ... 72s Selecting previously unselected package python3-brotli. 72s Preparing to unpack .../062-python3-brotli_1.1.0-2build5_amd64.deb ... 72s Unpacking python3-brotli (1.1.0-2build5) ... 72s Selecting previously unselected package python3-platformdirs. 72s Preparing to unpack .../063-python3-platformdirs_4.3.7-1_all.deb ... 72s Unpacking python3-platformdirs (4.3.7-1) ... 72s Selecting previously unselected package python3-fs. 72s Preparing to unpack .../064-python3-fs_2.4.16-7_all.deb ... 72s Unpacking python3-fs (2.4.16-7) ... 72s Selecting previously unselected package libxslt1.1:amd64. 72s Preparing to unpack .../065-libxslt1.1_1.1.43-0.1_amd64.deb ... 72s Unpacking libxslt1.1:amd64 (1.1.43-0.1) ... 72s Selecting previously unselected package python3-lxml:amd64. 72s Preparing to unpack .../066-python3-lxml_6.0.1-1_amd64.deb ... 72s Unpacking python3-lxml:amd64 (6.0.1-1) ... 72s Selecting previously unselected package python3-lz4. 72s Preparing to unpack .../067-python3-lz4_4.4.0+dfsg-2_amd64.deb ... 72s Unpacking python3-lz4 (4.4.0+dfsg-2) ... 72s Selecting previously unselected package python3-decorator. 72s Preparing to unpack .../068-python3-decorator_5.2.1-2_all.deb ... 72s Unpacking python3-decorator (5.2.1-2) ... 72s Selecting previously unselected package python3-scipy. 72s Preparing to unpack .../069-python3-scipy_1.15.3-1_amd64.deb ... 72s Unpacking python3-scipy (1.15.3-1) ... 72s Selecting previously unselected package python3-mpmath. 72s Preparing to unpack .../070-python3-mpmath_1.3.0-1_all.deb ... 72s Unpacking python3-mpmath (1.3.0-1) ... 72s Selecting previously unselected package python3-sympy. 72s Preparing to unpack .../071-python3-sympy_1.13.3-5_all.deb ... 72s Unpacking python3-sympy (1.13.3-5) ... 72s Selecting previously unselected package python3-ufolib2. 72s Preparing to unpack .../072-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 72s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 72s Selecting previously unselected package python3-unicodedata2. 72s Preparing to unpack .../073-python3-unicodedata2_15.1.0+ds-1build3_amd64.deb ... 72s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 72s Selecting previously unselected package libzopfli1. 72s Preparing to unpack .../074-libzopfli1_1.0.3-3_amd64.deb ... 72s Unpacking libzopfli1 (1.0.3-3) ... 72s Selecting previously unselected package python3-zopfli. 72s Preparing to unpack .../075-python3-zopfli_0.2.3.post1-1_amd64.deb ... 72s Unpacking python3-zopfli (0.2.3.post1-1) ... 72s Selecting previously unselected package unicode-data. 72s Preparing to unpack .../076-unicode-data_15.1.0-1_all.deb ... 72s Unpacking unicode-data (15.1.0-1) ... 72s Selecting previously unselected package python3-fonttools. 72s Preparing to unpack .../077-python3-fonttools_4.57.0-1_amd64.deb ... 72s Unpacking python3-fonttools (4.57.0-1) ... 73s Selecting previously unselected package python3-kiwisolver. 73s Preparing to unpack .../078-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 73s Unpacking python3-kiwisolver (1.4.7-3build1) ... 73s Selecting previously unselected package python3-packaging. 73s Preparing to unpack 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(2.1-6.1ubuntu2) ... 76s Setting up python3-platformdirs (4.3.7-1) ... 76s Setting up python3-fs (2.4.16-7) ... 76s Setting up unicode-data (15.1.0-1) ... 76s Setting up python3-decorator (5.2.1-2) ... 76s Setting up zip (3.0-15ubuntu2) ... 76s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 76s Setting up libblas3:amd64 (3.12.1-6build1) ... 76s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 76s Setting up python3-packaging (25.0-1) ... 76s Setting up libzopfli1 (1.0.3-3) ... 76s Setting up libnspr4:amd64 (2:4.36-1ubuntu2) ... 76s Setting up python3-brotli (1.1.0-2build5) ... 76s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 76s Setting up python3-cycler (0.12.1-1) ... 76s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 76s Setting up fonts-dejavu-mono (2.37-8) ... 76s Setting up python3-kiwisolver (1.4.7-3build1) ... 77s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 77s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 77s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 77s Setting up fonts-dejavu-core (2.37-8) ... 77s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 77s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 77s Setting up libwebp7:amd64 (1.5.0-0.1) ... 77s Setting up libxslt1.1:amd64 (1.1.43-0.1) ... 77s Setting up libhts3t64:amd64 (1.21+ds-1) ... 77s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 77s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 77s Setting up libthai-data (0.1.29-2build1) ... 77s Setting up python3-dateutil (2.9.0-4) ... 77s Setting up sgml-base (1.31+nmu1) ... 77s Setting up libgpgme11t64:amd64 (1.24.2-3ubuntu1) ... 77s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 77s Setting up libicu76:amd64 (76.1-4ubuntu2) ... 77s Setting up libpaper2:amd64 (2.2.5-0.3) ... 77s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 77s Setting up python3-mpmath (1.3.0-1) ... 77s Setting up python-matplotlib-data (3.10.1+dfsg1-4) ... 77s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 77s Setting up xdg-utils (1.2.1-2ubuntu1) ... 77s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 77s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 77s Setting up python3-pyfaidx (0.8.1.3-2) ... 77s Setting up python3-sympy (1.13.3-5) ... 81s Setting up libgpgmepp6t64:amd64 (1.24.2-3ubuntu1) ... 81s Setting up libice6:amd64 (2:1.1.1-1) ... 81s Setting up liblapack3:amd64 (3.12.1-6build1) ... 81s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 81s Setting up python3-pysam (0.23.0+ds-1build1) ... 81s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 81s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 81s Setting up libnss3:amd64 (2:3.114-1) ... 81s Setting up libpaper-utils (2.2.5-0.3) ... 81s Setting up xfonts-utils (1:7.7+7) ... 81s Setting up python3-zopfli (0.2.3.post1-1) ... 81s Setting up libthai0:amd64 (0.1.29-2build1) ... 81s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 81s Setting up libraqm0:amd64 (0.10.3-1) ... 81s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 82s Setting up python3-lxml:amd64 (6.0.1-1) ... 82s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 82s Setting up xml-core (0.19) ... 82s Setting up python3-contourpy (1.3.1-1build1) ... 82s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 82s Setting up libsm6:amd64 (2:1.2.6-1) ... 82s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 85s Regenerating fonts cache... done. 85s Setting up libxft2:amd64 (2.3.6-1build1) ... 85s Setting up python3-scipy (1.15.3-1) ... 86s Setting up libpoppler147:amd64 (25.03.0-10) ... 86s Setting up python3-pomegranate (0.15.0-1build1) ... 87s Setting up libtk8.6:amd64 (8.6.17-1) ... 87s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... 87s Setting up libpango-1.0-0:amd64 (1.56.3-1build1) ... 87s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 87s Setting up fonts-urw-base35 (20200910-8) ... 87s Setting up libcairo2:amd64 (1.18.4-1build1) ... 87s Setting up python3.13-tk (3.13.7-1) ... 87s Setting up python3-pil:amd64 (11.3.0-1ubuntu1) ... 87s Setting up python3-pandas (2.2.3+dfsg-9) ... 89s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 89s Setting up python3-sklearn (1.4.2+dfsg-8) ... 91s Setting up poppler-utils (25.03.0-10) ... 91s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1build1) ... 91s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1build1) ... 91s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 91s Setting up python3-cairo (1.27.0-2) ... 91s Setting up blt (2.5.3+dfsg-8) ... 91s Setting up python3-tk:amd64 (3.13.5-1) ... 91s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu1) ... 91s Setting up python3-rlpycairo (0.3.0-3) ... 91s Setting up r-base-core (4.5.1-1) ... 91s Creating config file /etc/R/Renviron with new version 91s Setting up python3-reportlab (4.4.2-1) ... 91s Setting up r-bioc-biocgenerics (0.52.0-2) ... 91s Setting up r-bioc-dnacopy (1.80.0-2) ... 91s Setting up python3-fonttools (4.57.0-1) ... 92s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 92s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 93s Processing triggers for man-db (2.13.1-1) ... 93s Processing triggers for install-info (7.1.1-1ubuntu1) ... 93s Processing triggers for libc-bin (2.42-0ubuntu3) ... 93s Processing triggers for sgml-base (1.31+nmu1) ... 93s Setting up w3c-sgml-lib (1.3-3) ... 109s Setting up python3-biopython (1.85+dfsg-4) ... 109s Setting up cnvkit (0.9.12-1) ... 110s autopkgtest [15:55:15]: test environment configured for cross building 110s autopkgtest [15:55:15]: test run-unit-test: [----------------------- 111s cnvkit.py batch -n -f formats/chrM-Y-trunc.hg19.fa -m wgs formats/na12878-chrM-Y-trunc.bam -d build 112s CNVkit 0.9.12 112s WGS protocol: recommend '--annotate' option (e.g. refFlat.txt) to help locate genes in output files. 112s chrM: Scanning for accessible regions 112s Accessible region chrM:0-121 (size 121) 112s Accessible region chrM:122-1271 (size 1149) 112s Accessible region chrM:1274-1288 (size 14) 112s Accessible region chrM:1289-1547 (size 258) 112s Accessible region chrM:1553-16571 (size 15018) 112s chrY: Scanning for accessible regions 112s Accessible region chrY:500-14900 (size 14400) 112s Accessible region chrY:15600-22966 (size 7366) 112s chrY: Joining over small gaps 112s Joining chrY 500-14900 and 15600-22966 (gap size 700) 112s Wrote chrM-Y-trunc.hg19.bed with 1 regions 112s Detected file format: bed 112s Splitting large targets 112s Created directory build 112s Wrote build/chrM-Y-trunc.hg19.target.bed with 4 regions 112s Wrote build/chrM-Y-trunc.hg19.antitarget.bed with 0 regions 112s Building a flat reference... 112s Detected file format: bed 112s Calculating GC and RepeatMasker content in formats/chrM-Y-trunc.hg19.fa ... 112s Extracting sequences from chromosome chrY 112s Wrote build/reference.cnn with 4 regions 112s Running 1 samples in serial 112s Running the CNVkit pipeline on formats/na12878-chrM-Y-trunc.bam ... 112s Indexing BAM file formats/na12878-chrM-Y-trunc.bam 112s Processing reads in na12878-chrM-Y-trunc.bam 112s Time: 0.005 seconds (7519 reads/sec, 813 bins/sec) 112s Summary: #bins=4, #reads=37, mean=9.2500, min=0.0, max=21.0 112s Percent reads in regions: 0.063 (of 58636 mapped) 112s Wrote build/na12878-chrM-Y-trunc.targetcoverage.cnn with 4 regions 112s Skip processing na12878-chrM-Y-trunc.bam with empty regions file build/chrM-Y-trunc.hg19.antitarget.bed 112s Wrote build/na12878-chrM-Y-trunc.antitargetcoverage.cnn with 0 regions 112s Processing target: na12878-chrM-Y-trunc 112s Keeping 4 of 4 bins 112s Correcting for GC bias... 112s Processing antitarget: na12878-chrM-Y-trunc 112s Wrote build/na12878-chrM-Y-trunc.cnr with 4 regions 112s Segmenting build/na12878-chrM-Y-trunc.cnr ... 112s Segmenting with method 'cbs', significance threshold 1e-06, in 1 processes 112s Post-processing build/na12878-chrM-Y-trunc.cns ... 112s Wrote build/na12878-chrM-Y-trunc.cns with 1 regions 112s Applying filter 'ci' 112s Filtered by 'ci' from 1 to 1 rows 112s Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 112s Wrote build/na12878-chrM-Y-trunc.call.cns with 1 regions 112s Significant hits in 4/4 bins (100%) 112s Wrote build/na12878-chrM-Y-trunc.bintest.cns with 4 regions 112s 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/ 113s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 113s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 113s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 113s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 113s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 113s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 113s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 113s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 113s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 113s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 114s Number of target and antitarget files: 3, 3 114s No FASTA reference genome provided; skipping GC, RM calculations 114s Sample sex not provided; inferring from samples. 114s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 114s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 114s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 114s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 114s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 114s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 114s Loading build/p2-20_5.targetcoverage.cnn 114s Correcting for GC bias for p2-20_5... 115s Correcting for density bias for p2-20_5... 115s Loading build/p2-5_5.targetcoverage.cnn 115s Correcting for GC bias for p2-5_5... 115s Correcting for density bias for p2-5_5... 115s Loading build/p2-9_5.targetcoverage.cnn 115s Correcting for GC bias for p2-9_5... 115s Correcting for density bias for p2-9_5... 115s Loading build/p2-20_5.antitargetcoverage.cnn 115s Correcting for GC bias for p2-20_5... 115s Loading build/p2-5_5.antitargetcoverage.cnn 115s Correcting for GC bias for p2-5_5... 115s Loading build/p2-9_5.antitargetcoverage.cnn 115s Correcting for GC bias for p2-9_5... 115s Calculating average bin coverages 118s Calculating bin spreads 118s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 118s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 118s " chr1:2435319-2436685 log2=-0.709 spread=0.503 118s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 118s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 118s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 118s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 118s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 118s " chr1:120611883-120612051 log2=0.070 spread=0.050 118s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 118s " chr1:156842391-156842479 log2=-0.398 spread=0.290 118s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 118s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 118s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 118s " chr1:183481886-183481951 log2=-0.040 spread=0.119 118s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 118s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 118s " chr1:243800859-243801066 log2=0.023 spread=0.063 118s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 118s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 118s " chr2:25536716-25536891 log2=0.702 spread=0.033 118s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 118s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 118s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 118s REL chr2:61108881-61109061 log2=1.026 spread=0.559 118s " chr2:61128072-61128256 log2=0.115 spread=0.173 118s " chr2:61145275-61145462 log2=0.014 spread=0.099 118s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 118s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 118s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 118s " chr2:128095237-128095425 log2=0.215 spread=0.212 118s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 118s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 118s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 118s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 118s " chr3:97160189-97160367 log2=-0.050 spread=0.191 118s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 118s " chr3:142286854-142287031 log2=-0.076 spread=0.116 118s GAK chr4:896278-896357 log2=-1.505 spread=1.261 118s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 118s " chr4:1803044-1803507 log2=-0.073 spread=0.117 118s " chr4:1808792-1809022 log2=0.252 spread=0.108 118s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 118s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 118s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 118s " chr4:178514600-178514725 log2=-0.098 spread=0.096 118s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 118s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 118s " chr5:1295312-1295381 log2=-0.690 spread=0.462 118s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 118s " chr5:25519857-25520034 log2=-0.015 spread=0.095 118s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 118s " chr5:38962338-38962525 log2=0.005 spread=0.019 118s " chr5:38966685-38966862 log2=0.006 spread=0.165 118s " chr5:38978620-38978763 log2=0.040 spread=0.030 118s " chr5:39074133-39074327 log2=-0.158 spread=0.139 118s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 118s " chr5:51030131-51030313 log2=-0.034 spread=0.192 118s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 118s " chr5:56168412-56168590 log2=0.479 spread=0.038 118s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 118s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 118s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 118s " chr5:86637023-86637168 log2=0.054 spread=0.111 118s " chr5:86642414-86642592 log2=0.254 spread=0.162 118s " chr5:86648912-86649096 log2=0.092 spread=0.062 118s " chr5:86670598-86670778 log2=0.222 spread=0.198 118s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 118s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 118s APC chr5:112101965-112102138 log2=0.104 spread=0.217 118s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 118s " chr5:170837567-170837631 log2=0.085 spread=0.349 118s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 118s " chr5:180046203-180046404 log2=-1.531 spread=0.722 118s " chr5:180076418-180076603 log2=-2.224 spread=1.416 118s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 118s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 118s " chr6:31939599-31940313 log2=-19.582 spread=0.181 118s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 118s " chr6:31946632-31946824 log2=-20.052 spread=0.088 118s " chr6:31947142-31947366 log2=-20.114 spread=0.066 118s " chr6:31948176-31948360 log2=-19.982 spread=0.149 118s " chr6:31948382-31948612 log2=-19.757 spread=0.165 118s " chr6:31948730-31949253 log2=-20.048 spread=0.014 118s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 118s " chr6:32164046-32164227 log2=-19.755 spread=0.189 118s " chr6:32164652-32164888 log2=-19.984 spread=0.154 118s " chr6:32165021-32165403 log2=-19.625 spread=0.196 118s " chr6:32166163-32166545 log2=-20.043 spread=0.072 118s " chr6:32166648-32166962 log2=-3.514 spread=5.742 118s " chr6:32168554-32168821 log2=-19.601 spread=0.197 118s " chr6:32168844-32169306 log2=-19.683 spread=0.166 118s " chr6:32169801-32170391 log2=-19.405 spread=0.205 118s " chr6:32171492-32171691 log2=-20.095 spread=0.101 118s " chr6:32171861-32172198 log2=-3.141 spread=7.288 118s " chr6:32178478-32178749 log2=-19.927 spread=0.164 118s " chr6:32180197-32180441 log2=-10.902 spread=9.532 118s " chr6:32180544-32180722 log2=-19.675 spread=0.186 118s " chr6:32180857-32181062 log2=-19.562 spread=0.227 118s " chr6:32181411-32181646 log2=-19.966 spread=0.171 118s " chr6:32181832-32182066 log2=-19.961 spread=0.172 118s " chr6:32182948-32183194 log2=-19.935 spread=0.168 118s " chr6:32184667-32185079 log2=-19.923 spread=0.165 118s " chr6:32185720-32185919 log2=-19.707 spread=0.197 118s " chr6:32187317-32187601 log2=-19.765 spread=0.173 118s " chr6:32187871-32188094 log2=-19.660 spread=0.188 118s " chr6:32188127-32188451 log2=-19.622 spread=0.169 118s " chr6:32188481-32188693 log2=-19.902 spread=0.132 118s " chr6:32188704-32189133 log2=-19.501 spread=0.193 118s " chr6:32190258-32190616 log2=-19.570 spread=0.209 118s " chr6:32190724-32190908 log2=-19.540 spread=0.232 118s " chr6:32191570-32191668 log2=-19.773 spread=0.178 118s " chr6:32191676-32191753 log2=-19.374 spread=0.201 118s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 118s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 118s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 118s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 118s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 118s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 118s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 118s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 118s " chr6:128316545-128316699 log2=-0.070 spread=0.050 118s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 118s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 118s " chr6:157099442-157099991 log2=-0.846 spread=0.504 118s " chr6:157100042-157100634 log2=-1.570 spread=0.825 118s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 118s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 118s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 118s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 118s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 118s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 118s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 118s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 118s " chr7:98491365-98491541 log2=0.209 spread=0.153 118s " chr7:98493314-98493496 log2=0.389 spread=0.207 118s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 118s " chr7:128829048-128829358 log2=-0.474 spread=0.315 118s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 118s " chr7:140484736-140484912 log2=0.081 spread=0.150 118s " chr7:140487956-140488430 log2=-0.089 spread=0.142 118s " chr7:140493336-140493442 log2=-0.340 spread=0.283 118s " chr7:140624315-140624540 log2=-0.497 spread=0.342 118s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 118s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 118s " chr8:30941153-30941335 log2=0.079 spread=0.294 118s " chr8:30942625-30942802 log2=0.044 spread=0.247 118s " chr8:30947918-30948092 log2=0.151 spread=0.124 118s " chr8:31000128-31000252 log2=-0.099 spread=0.098 118s " chr8:31001006-31001182 log2=-0.002 spread=0.062 118s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 118s " chr8:37698557-37699898 log2=-0.612 spread=0.029 118s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 118s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 118s " chr8:48845528-48845758 log2=0.056 spread=0.196 118s " chr8:48866846-48867043 log2=-0.067 spread=0.097 118s " chr8:48868369-48868526 log2=-0.239 spread=0.174 118s " chr8:48872485-48872722 log2=-0.636 spread=0.464 118s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 118s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 118s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 118s " chr9:2101491-2101640 log2=0.244 spread=0.104 118s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 118s " chr9:5067014-5067883 log2=0.146 spread=0.089 118s " chr9:5068184-5070306 log2=0.133 spread=0.092 118s " chr9:5076944-5077152 log2=0.046 spread=0.137 118s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 118s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 118s " chr9:21986759-21986899 log2=0.058 spread=0.175 118s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 118s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 118s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 118s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 118s " chr9:87425375-87425452 log2=0.494 spread=0.066 118s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 118s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 118s " chr9:139250747-139251032 log2=-0.223 spread=0.273 118s " chr9:139252418-139252703 log2=-0.512 spread=0.264 118s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 118s " chr9:139417262-139417677 log2=-0.173 spread=0.191 118s " chr9:139440110-139440287 log2=-1.257 spread=0.500 118s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 118s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 118s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 118s " chr10:43600360-43600677 log2=-0.341 spread=0.222 118s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 118s " chr10:89685254-89685374 log2=0.244 spread=0.259 118s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 118s " chr10:93579008-93579121 log2=0.166 spread=0.220 118s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 118s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 118s " chr10:112679716-112679934 log2=-0.008 spread=0.028 118s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 118s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 118s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 118s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 118s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 118s " chr11:94170270-94170454 log2=0.095 spread=0.285 118s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 118s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 118s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 118s " chr11:108164020-108164234 log2=-0.056 spread=0.040 118s " chr11:108217986-108218135 log2=0.359 spread=0.277 118s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 118s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 118s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 118s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 118s " chr12:25391004-25391186 log2=0.368 spread=0.128 118s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 118s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 118s " chr12:51206782-51207287 log2=-0.012 spread=0.101 118s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 118s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 118s " chr13:26970356-26970536 log2=0.137 spread=0.121 118s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 118s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 118s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 118s " chr13:32903506-32903689 log2=0.019 spread=0.232 118s " chr13:32918645-32918823 log2=0.158 spread=0.114 118s " chr13:32920899-32921077 log2=0.014 spread=0.247 118s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 118s " chr13:48919164-48919369 log2=0.025 spread=0.094 118s " chr13:48921877-48922044 log2=0.106 spread=0.147 118s " chr13:48923026-48923204 log2=0.360 spread=0.016 118s " chr13:48938965-48939147 log2=0.084 spread=0.356 118s " chr13:48941578-48941767 log2=0.238 spread=0.212 118s " chr13:48947486-48947665 log2=0.025 spread=0.126 118s " chr13:48954166-48954251 log2=0.061 spread=0.273 118s " chr13:49037815-49038005 log2=0.063 spread=0.062 118s " chr13:49047410-49047589 log2=0.053 spread=0.170 118s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 118s " chr13:85527771-85527948 log2=0.007 spread=0.222 118s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 118s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 118s " chr13:110438332-110438432 log2=-3.643 spread=2.325 118s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 118s " chr14:20291466-20291612 log2=0.697 spread=0.248 118s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 118s " chr14:36989195-36989373 log2=0.023 spread=0.162 118s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 118s " chr14:50619741-50619923 log2=0.003 spread=0.272 118s " chr14:50697856-50698044 log2=0.277 spread=0.334 118s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 118s " chr14:71275790-71275923 log2=-2.815 spread=1.938 118s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 118s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 118s " chr15:38544477-38545455 log2=-0.348 spread=0.179 118s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 118s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 118s " chr15:41803968-41804185 log2=-2.202 spread=0.188 118s " chr15:41804261-41804494 log2=-0.402 spread=0.392 118s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 118s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 118s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 118s " chr16:2611404-2611585 log2=-5.171 spread=1.963 118s " chr16:2611721-2611943 log2=-11.810 spread=9.172 118s " chr16:2615504-2615725 log2=-20.113 spread=0.007 118s " chr16:2616307-2616486 log2=-20.054 spread=0.072 118s " chr16:2631267-2631414 log2=-20.009 spread=0.061 118s " chr16:2631583-2631734 log2=-20.089 spread=0.090 118s " chr16:2633363-2633616 log2=-20.101 spread=0.089 118s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 118s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 118s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 118s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 118s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 118s " chr16:50826460-50826650 log2=0.239 spread=0.204 118s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 118s " chr16:60005694-60005857 log2=-0.366 spread=0.298 118s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 118s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 118s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 118s " chr17:12011053-12011253 log2=0.028 spread=0.232 118s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 118s " chr17:29496854-29497046 log2=0.226 spread=0.193 118s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 118s " chr17:30519172-30519355 log2=0.163 spread=0.289 118s " chr17:30525911-30526093 log2=-0.157 spread=0.046 118s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 118s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 118s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 118s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 118s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 118s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 118s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 118s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 118s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 118s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 118s " chr19:2210351-2210545 log2=-0.860 spread=0.261 118s " chr19:2226130-2227152 log2=-0.113 spread=0.120 118s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 118s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 118s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 118s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 118s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 118s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 118s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 118s " chr19:15311544-15311749 log2=-1.887 spread=1.202 118s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 118s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 118s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 118s " chr19:33792774-33793010 log2=-1.781 spread=0.127 118s " chr19:33793014-33793356 log2=-0.541 spread=0.385 118s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 118s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 118s " chr19:45873698-45873881 log2=-0.522 spread=0.327 118s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 118s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 118s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 118s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 118s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 118s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 118s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 118s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 118s " chr21:36265140-36265318 log2=0.042 spread=0.039 118s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 118s " chr22:29115325-29115465 log2=0.055 spread=0.390 118s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 118s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 118s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 118s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 118s " chrX:1317372-1317594 log2=-21.121 spread=0.049 118s " chrX:1321225-1321435 log2=-20.851 spread=0.196 118s " chrX:1325274-1325530 log2=-21.121 spread=0.011 118s " chrX:1327651-1327830 log2=-21.000 spread=0.029 118s " chrX:1331391-1331576 log2=-21.018 spread=0.052 118s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 118s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 118s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 118s " chrX:123185143-123185290 log2=-1.018 spread=0.062 118s " chrX:123202378-123202544 log2=-0.959 spread=0.103 118s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 118s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 118s " chrY:9008607-9008759 log2=-1.012 spread=0.097 118s " chrY:13131970-13132039 log2=-1.004 spread=0.074 118s " chrY:19506485-19506650 log2=-1.018 spread=0.034 118s " chrY:21033918-21034071 log2=-1.013 spread=0.057 118s " chrY:28463435-28463622 log2=-0.952 spread=0.039 118s " chrY:28514033-28514208 log2=-0.992 spread=0.026 118s Antitargets: 108 (0.8597%) bins failed filters 118s Wrote build/reference-picard.cnn with 19209 regions 118s 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 119s Processing target: p2-5_5 119s Keeping 6308 of 6646 bins 119s Correcting for GC bias... 119s Correcting for density bias... 119s Processing antitarget: p2-5_5 119s Keeping 12455 of 12563 bins 119s Correcting for GC bias... 119s WARNING: Skipping correction for RepeatMasker bias 119s Targets are 1.18 x more variable than antitargets 119s Wrote build/p2-5_5.cnr with 18763 regions 120s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 121s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 121s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 121s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 122s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 122s 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 123s Processing target: p2-9_2 123s Keeping 6308 of 6646 bins 123s Correcting for GC bias... 123s Correcting for density bias... 123s Processing antitarget: p2-9_2 123s Keeping 12455 of 12563 bins 123s Correcting for GC bias... 123s WARNING: Skipping correction for RepeatMasker bias 123s Targets are 1.72 x more variable than antitargets 123s Wrote build/p2-9_2.cnr with 18763 regions 123s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 124s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 124s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 124s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 125s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 125s 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 126s Processing target: p2-20_1 126s Keeping 6308 of 6646 bins 126s Correcting for GC bias... 126s Correcting for density bias... 126s Processing antitarget: p2-20_1 126s Keeping 12455 of 12563 bins 126s Correcting for GC bias... 126s WARNING: Skipping correction for RepeatMasker bias 126s Targets are 1.12 x more variable than antitargets 127s Wrote build/p2-20_1.cnr with 18763 regions 127s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 128s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 128s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 128s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 129s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 129s 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 130s Processing target: p2-20_2 130s Keeping 6308 of 6646 bins 130s Correcting for GC bias... 130s Correcting for density bias... 130s Processing antitarget: p2-20_2 130s Keeping 12455 of 12563 bins 130s Correcting for GC bias... 130s WARNING: Skipping correction for RepeatMasker bias 130s Targets are 1.10 x more variable than antitargets 130s Wrote build/p2-20_2.cnr with 18763 regions 130s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 131s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 131s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 131s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 132s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 132s 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 133s Processing target: p2-20_3 133s Keeping 6308 of 6646 bins 133s Correcting for GC bias... 133s Correcting for density bias... 133s Processing antitarget: p2-20_3 133s Keeping 12455 of 12563 bins 133s Correcting for GC bias... 133s WARNING: Skipping correction for RepeatMasker bias 133s Antitargets are 1.09 x more variable than targets 133s Wrote build/p2-20_3.cnr with 18763 regions 134s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 135s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 135s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 135s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 136s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 136s 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 137s Processing target: p2-20_4 137s Keeping 6308 of 6646 bins 137s Correcting for GC bias... 137s Correcting for density bias... 137s Processing antitarget: p2-20_4 137s Keeping 12455 of 12563 bins 137s Correcting for GC bias... 137s WARNING: Skipping correction for RepeatMasker bias 137s Targets are 1.43 x more variable than antitargets 137s Wrote build/p2-20_4.cnr with 18763 regions 137s 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 138s Processing target: p2-20_5 138s Keeping 6308 of 6646 bins 138s Correcting for GC bias... 138s Correcting for density bias... 138s Processing antitarget: p2-20_5 138s Keeping 12455 of 12563 bins 138s Correcting for GC bias... 138s WARNING: Skipping correction for RepeatMasker bias 138s Targets are 2.50 x more variable than antitargets 138s Wrote build/p2-20_5.cnr with 18763 regions 139s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 139s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 143s Dropped 8 / 49 bins on chromosome chrY 143s Wrote build/p2-5_5.cns with 71 regions 143s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 144s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 145s Dropped 1 / 949 bins on chromosome chr6 148s Dropped 27 / 49 bins on chromosome chrY 148s Wrote build/p2-9_2.cns with 103 regions 148s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 149s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 153s Dropped 6 / 49 bins on chromosome chrY 153s Wrote build/p2-20_1.cns with 121 regions 153s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 154s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 158s Dropped 7 / 49 bins on chromosome chrY 158s Wrote build/p2-20_2.cns with 117 regions 158s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 159s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 163s Dropped 11 / 49 bins on chromosome chrY 163s Wrote build/p2-20_3.cns with 64 regions 163s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 164s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 168s Dropped 8 / 49 bins on chromosome chrY 168s Wrote build/p2-20_4.cns with 143 regions 169s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 169s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 173s Smoothing overshot at 1 / 123 indices: (-0.30060035404086394, 0.32508880185194683) vs. original (-0.363302, 0.311218) 173s Dropped 6 / 49 bins on chromosome chrY 173s Wrote build/p2-20_5.cns with 120 regions 174s 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 175s Wrote p2-5_5-scatter.pdf 175s 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 176s Smoothing overshot at 3 / 97 indices: (-19.90010586862171, -3.3099069223720505) vs. original (-19.294, -0.16431) 177s Wrote p2-9_2-scatter.pdf 177s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 178s Showing 1480 probes and 0 selected genes in region chr1 178s Wrote p2-9_2-chr1-scatter.pdf 178s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 179s Showing 201 probes and 0 selected genes in region chr21 179s Wrote p2-9_2-chr21-scatter.pdf 179s 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 180s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 180s Wrote p2-9_2-chr9p-scatter.pdf 181s 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 181s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 181s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 182s 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 183s Detected file format: bed 183s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 183s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 183s 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 183s /usr/bin/pdfunite 183s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 184s Treating sample p2-5_5 as female 188s Wrote p2-5_5-diagram.pdf 188s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 189s Treating sample p2-9_2 as female 193s Wrote p2-9_2-diagram.pdf 193s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 194s Treating sample p2-20_1 as female 198s Wrote p2-20_1-diagram.pdf 198s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 199s Treating sample p2-20_2 as female 203s Wrote p2-20_2-diagram.pdf 203s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 204s Treating sample p2-5_5 as female 204s Wrote p2-5_5-cbs-diagram.pdf 204s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 205s Treating sample p2-9_2 as female 205s Wrote p2-9_2-cbs-diagram.pdf 205s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 206s Treating sample p2-20_1 as female 206s Wrote p2-20_1-cbs-diagram.pdf 206s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 207s Treating sample p2-20_2 as female 207s Wrote p2-20_2-cbs-diagram.pdf 208s 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 208s Treating sample p2-5_5 as female 211s Wrote p2-5_5-both-diagram.pdf 211s 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 212s Treating sample p2-9_2 as female 215s Wrote p2-9_2-both-diagram.pdf 215s 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 216s Treating sample p2-20_1 as female 218s Wrote p2-20_1-both-diagram.pdf 218s 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 219s Treating sample p2-20_2 as female 222s Wrote p2-20_2-both-diagram.pdf 222s 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 222s /usr/bin/pdfunite 222s 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 223s Treating sample p2-5_5 as female 223s Treating sample p2-9_2 as female 223s Treating sample p2-20_1 as female 223s Treating sample p2-20_2 as female 223s Treating sample p2-20_3 as female 223s Treating sample p2-20_4 as female 223s Treating sample p2-20_5 as female 224s Wrote heatmap-picard.pdf 224s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 225s Found 14 gene breakpoints 225s Wrote p2-9_2-breaks.txt 225s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 226s Treating sample p2-9_2 as female 227s Found 323 gene-level gains and losses 227s Wrote p2-9_2-genemetrics.txt 227s 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 228s Wrote gender-picard.txt 228s 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 230s Wrote p2-all.cdt 230s 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 233s Wrote p2-all-jtv.txt 233s 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 234s Wrote p2-all.seg 234s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 235s Wrote p2-9_2.nexus 235s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 236s Selected test sample NA12882 and control sample NA12878 236s Loaded 3654 records; skipped: 514 somatic, 394 depth 236s Kept 2631 heterozygous of 3654 VCF records 237s Placed 705 variants into 18763 bins 237s Wrote p2-9_2.nexus-ogt 237s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 238s Treating sample p2-5_5 as female 238s Rescaling sample with purity 0.65, ploidy 2 238s Wrote build/p2-5_5.call.cns with 71 regions 238s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 239s Treating sample p2-9_2 as female 239s Rescaling sample with purity 0.65, ploidy 2 239s Wrote build/p2-9_2.call.cns with 103 regions 239s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 240s Treating sample p2-20_1 as female 240s Rescaling sample with purity 0.65, ploidy 2 240s Wrote build/p2-20_1.call.cns with 121 regions 240s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 241s Treating sample p2-20_2 as female 241s Rescaling sample with purity 0.65, ploidy 2 241s Wrote build/p2-20_2.call.cns with 117 regions 241s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 242s Treating sample p2-20_3 as female 242s Rescaling sample with purity 0.65, ploidy 2 242s Wrote build/p2-20_3.call.cns with 64 regions 242s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 243s Treating sample p2-20_4 as female 243s Rescaling sample with purity 0.65, ploidy 2 243s Wrote build/p2-20_4.call.cns with 143 regions 243s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 244s Treating sample p2-20_5 as female 244s Rescaling sample with purity 0.65, ploidy 2 244s Wrote build/p2-20_5.call.cns with 120 regions 244s 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 245s Treating sample p2-5_5.call as female 245s Treating sample p2-9_2.call as female 245s Treating sample p2-20_1.call as female 245s Treating sample p2-20_2.call as female 245s Treating sample p2-20_3.call as female 245s Treating sample p2-20_4.call as female 245s Treating sample p2-20_5.call as female 245s Wrote p2-all.bed 245s 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 246s Treating sample p2-9_2.call as female 246s Wrote p2-9_2.vcf 246s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 247s Wrote p2-9_2.theta2.input 248s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 248s --mean --median --mode --t-test \ 248s --stdev --mad --mse --iqr --bivar \ 248s --ci --pi --sem --smooth-bootstrap 249s Wrote p2-9_2-segmetrics.cns with 103 regions 249s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 249s --ci -b 50 -a 0.5 250s Wrote p2-5_5-segmetrics.cns with 71 regions 250s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 251s Wrote p2-5_5-metrics.tsv 251s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 252s Wrote p2-9_2-metrics.tsv 252s 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 253s Wrote p2-20-metrics.tsv 253s PASS 254s autopkgtest [15:57:39]: test run-unit-test: -----------------------] 254s run-unit-test PASS 254s autopkgtest [15:57:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 254s autopkgtest [15:57:39]: test pybuild-autopkgtest: preparing testbed 260s Creating nova instance adt-resolute-i386-cnvkit-20251018-155325-juju-7f2275-prod-proposed-migration-environment-20-e1262310-29d4-4b01-b022-253b9a6bfdfc from image adt/ubuntu-resolute-amd64-server-20251018.img (UUID dd697a48-b6cc-4a02-84bf-0f9f2fad5f89)... 290s autopkgtest [15:58:14]: testbed dpkg architecture: amd64 290s autopkgtest [15:58:14]: testbed apt version: 3.1.6ubuntu2 290s autopkgtest [15:58:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 290s autopkgtest [15:58:15]: testbed release detected to be: resolute 291s autopkgtest [15:58:16]: updating testbed package index (apt update) 291s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 291s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 291s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 291s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 291s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [28.4 kB] 291s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 291s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.4 kB] 291s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [345 kB] 291s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [85.2 kB] 291s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [46.6 kB] 291s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 291s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 291s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [233 kB] 291s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [87.6 kB] 291s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [2772 B] 291s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [8376 B] 291s Fetched 972 kB in 1s (1622 kB/s) 292s Reading package lists... 292s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 292s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 292s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 292s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 293s Reading package lists... 293s Reading package lists... 293s Building dependency tree... 293s Reading state information... 293s Calculating upgrade... 293s The following packages will be upgraded: 293s apt gir1.2-girepository-2.0 libapt-pkg7.0 libgirepository-1.0-1 293s libpython3-stdlib python3 python3-minimal 293s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 293s Need to get 2751 kB of archives. 293s After this operation, 2048 B of additional disk space will be used. 293s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.13.7-2 [27.8 kB] 293s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.13.7-2 [23.9 kB] 293s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.13.7-2 [10.6 kB] 293s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.8ubuntu1 [1140 kB] 293s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.8ubuntu1 [1438 kB] 294s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-1.0-1 amd64 1.86.0-6 [85.9 kB] 294s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-2.0 amd64 1.86.0-6 [25.3 kB] 294s dpkg-preconfigure: unable to re-open stdin: No such file or directory 294s Fetched 2751 kB in 0s (6655 kB/s) 294s (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 ... 78439 files and directories currently installed.) 294s Preparing to unpack .../python3-minimal_3.13.7-2_amd64.deb ... 294s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 294s Setting up python3-minimal (3.13.7-2) ... 294s (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 ... 78439 files and directories currently installed.) 294s Preparing to unpack .../0-python3_3.13.7-2_amd64.deb ... 294s running python pre-rtupdate hooks for python3.13... 294s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 294s Preparing to unpack .../1-libpython3-stdlib_3.13.7-2_amd64.deb ... 294s Unpacking libpython3-stdlib:amd64 (3.13.7-2) over (3.13.7-1) ... 294s Preparing to unpack .../2-libapt-pkg7.0_3.1.8ubuntu1_amd64.deb ... 294s Unpacking libapt-pkg7.0:amd64 (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 294s Preparing to unpack .../3-apt_3.1.8ubuntu1_amd64.deb ... 294s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 294s Preparing to unpack .../4-libgirepository-1.0-1_1.86.0-6_amd64.deb ... 294s Unpacking libgirepository-1.0-1:amd64 (1.86.0-6) over (1.84.0-1) ... 294s Preparing to unpack .../5-gir1.2-girepository-2.0_1.86.0-6_amd64.deb ... 294s Unpacking gir1.2-girepository-2.0:amd64 (1.86.0-6) over (1.84.0-1) ... 294s Setting up libgirepository-1.0-1:amd64 (1.86.0-6) ... 294s Setting up libapt-pkg7.0:amd64 (3.1.8ubuntu1) ... 294s Setting up libpython3-stdlib:amd64 (3.13.7-2) ... 294s Setting up apt (3.1.8ubuntu1) ... 295s Setting up python3 (3.13.7-2) ... 295s running python rtupdate hooks for python3.13... 295s running python post-rtupdate hooks for python3.13... 295s Setting up gir1.2-girepository-2.0:amd64 (1.86.0-6) ... 295s Processing triggers for man-db (2.13.1-1) ... 296s Processing triggers for libc-bin (2.42-0ubuntu3) ... 296s autopkgtest [15:58:21]: upgrading testbed (apt dist-upgrade and autopurge) 296s Reading package lists... 296s Building dependency tree... 296s Reading state information... 297s Calculating upgrade... 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 297s Reading package lists... 297s Building dependency tree... 297s Reading state information... 297s Solving dependencies... 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 297s autopkgtest [15:58:22]: rebooting testbed after setup commands that affected boot 313s Reading package lists... 313s Building dependency tree... 313s Reading state information... 313s Solving dependencies... 314s The following NEW packages will be installed: 314s autoconf automake autopoint autotools-dev binutils-i686-linux-gnu blt 314s build-essential cnvkit cpp cpp-15 cpp-15-i686-linux-gnu 314s cpp-15-x86-64-linux-gnu cpp-i686-linux-gnu cpp-x86-64-linux-gnu 314s crossbuild-essential-i386 cython3 debhelper debugedit dh-autoreconf 314s dh-python dh-strip-nondeterminism dwz fontconfig fontconfig-config 314s fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 g++ g++-15 314s g++-15-i686-linux-gnu g++-15-x86-64-linux-gnu g++-i686-linux-gnu 314s g++-x86-64-linux-gnu gcc gcc-11-base:i386 gcc-15 gcc-15-cross-base 314s gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base gcc-15-x86-64-linux-gnu 314s gcc-i686-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 314s libarchive-zip-perl libasan6:i386 libasan8 libasan8-i386-cross 314s libatomic1:i386 libatomic1-i386-cross libblas3 libc6-dev:i386 314s libc6-dev-i386-cross libc6-i386-cross libcairo2 libcc1-0 libcrypt-dev:i386 314s libcrypt1:i386 libdatrie1 libdebhelper-perl libdeflate0 314s libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 314s libgcc-11-dev:i386 libgcc-15-dev libgcc-15-dev-i386-cross 314s libgcc-s1-i386-cross libgfortran5 libgomp1 libgomp1:i386 libgomp1-i386-cross 314s libgpgme11t64 libgpgmepp6t64 libgraphite2-3 libharfbuzz0b libhts3t64 314s libhtscodecs2 libhwasan0 libice6 libicu76 libimagequant0 libisl23 libitm1 314s libitm1:i386 libitm1-i386-cross libjbig0 libjpeg-turbo8 libjpeg8 314s libjs-jquery libjs-jquery-ui liblapack3 liblcms2-2 liblerc4 liblsan0 libmpc3 314s libnspr4 libnss3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 314s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpoppler147 314s libpython3.14-minimal libpython3.14-stdlib libqhull-r8.0 libquadmath0 314s libquadmath0:i386 libquadmath0-i386-cross libraqm0 libsharpyuv0 libsm6 314s libstdc++-11-dev:i386 libstdc++-15-dev libstdc++-15-dev-i386-cross 314s libstdc++6:i386 libstdc++6-i386-cross libtcl8.6 libthai-data libthai0 314s libtiff6 libtk8.6 libtool libtsan2 libubsan1 libubsan1:i386 314s libubsan1-i386-cross libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 314s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 libzopfli1 314s linux-libc-dev:i386 linux-libc-dev-i386-cross m4 po-debconf poppler-utils 314s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python-matplotlib-data 314s python3-all python3-biopython python3-brotli python3-build python3-cairo 314s python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil 314s python3-decorator python3-fonttools python3-freetype python3-fs 314s python3-iniconfig python3-installer python3-joblib python3-kiwisolver 314s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-networkx 314s python3-numpy python3-numpy-dev python3-packaging python3-pandas 314s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 314s python3-pluggy python3-pomegranate python3-pyfaidx python3-pyproject-hooks 314s python3-pysam python3-pytest python3-pytz python3-reportlab 314s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 314s python3-sympy python3-threadpoolctl python3-tk python3-ufolib2 python3-wheel 314s python3-zopfli python3.13-tk python3.14 python3.14-minimal r-base-core 314s r-bioc-biocgenerics r-bioc-dnacopy sgml-base tk8.6-blt2.5 unicode-data unzip 314s w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 314s 0 upgraded, 215 newly installed, 0 to remove and 0 not upgraded. 314s Need to get 362 MB of archives. 314s After this operation, 1395 MB of additional disk space will be used. 314s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 314s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 314s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 314s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 315s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 315s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpython3.14-minimal amd64 3.14.0-1 [905 kB] 315s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3.14-minimal amd64 3.14.0-1 [2508 kB] 315s Get:8 http://ftpmaster.internal/ubuntu resolute/main i386 libcrypt1 i386 1:4.4.38-1build1 [91.8 kB] 315s Get:9 http://ftpmaster.internal/ubuntu resolute/main i386 libatomic1 i386 15.2.0-5ubuntu1 [8412 B] 315s Get:10 http://ftpmaster.internal/ubuntu resolute/main i386 libstdc++6 i386 15.2.0-5ubuntu1 [877 kB] 315s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.19-8 [248 kB] 315s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 315s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 316s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.17-4ubuntu1 [572 kB] 316s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.1-2build2 [619 kB] 316s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1036 kB] 316s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 316s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 316s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 316s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 316s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 316s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 316s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 316s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.15.0-2.3ubuntu1 [38.0 kB] 316s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.15.0-2.3ubuntu1 [141 kB] 316s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 316s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 316s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 316s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 316s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 316s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 316s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1 [685 kB] 316s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-1build3 [57.0 kB] 316s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-5ubuntu1 [12.9 MB] 317s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-5ubuntu1 [1028 B] 317s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 317s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 317s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-5ubuntu1 [47.4 kB] 317s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-5ubuntu1 [151 kB] 317s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-5ubuntu1 [29.3 kB] 317s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-5ubuntu1 [3071 kB] 317s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-5ubuntu1 [1360 kB] 317s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-5ubuntu1 [2757 kB] 317s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-5ubuntu1 [1210 kB] 317s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-5ubuntu1 [1685 kB] 317s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-5ubuntu1 [153 kB] 317s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-5ubuntu1 [2863 kB] 317s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-5ubuntu1 [25.4 MB] 318s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-5ubuntu1 [523 kB] 318s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 318s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 318s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-5ubuntu1 [2573 kB] 318s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-5ubuntu1 [14.4 MB] 318s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-5ubuntu1 [23.7 kB] 318s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 318s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 318s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 318s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-charset-normalizer amd64 3.4.2-1 [129 kB] 318s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] 318s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-tk amd64 3.13.5-1 [9916 B] 318s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pil.imagetk amd64 11.3.0-1ubuntu1 [9700 B] 318s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 318s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu2 [152 kB] 318s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 318s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 318s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [188 kB] 318s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 318s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 318s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libraqm0 amd64 0.10.3-1 [15.4 kB] 318s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 318s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 318s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 318s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 318s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 318s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 318s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 318s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 318s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pil amd64 11.3.0-1ubuntu1 [496 kB] 318s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 318s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2build1 [17.4 kB] 318s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2build1 [6120 B] 318s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-1build1 [611 kB] 318s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-cairo amd64 1.27.0-2 [124 kB] 318s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 318s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 318s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-reportlab all 4.4.2-1 [1145 kB] 318s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 318s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 318s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 318s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-biopython amd64 1.85+dfsg-4 [1719 kB] 318s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 318s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 318s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lyx all 2.4.4-1 [171 kB] 318s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 python-matplotlib-data all 3.10.1+dfsg1-4 [2930 kB] 318s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 318s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 318s Get:97 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 318s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-brotli amd64 1.1.0-2build5 [342 kB] 318s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.3.7-1 [16.9 kB] 318s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 318s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libxslt1.1 amd64 1.1.43-0.1 [172 kB] 318s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-lxml amd64 6.0.1-1 [1528 kB] 318s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-lz4 amd64 4.4.0+dfsg-2 [26.6 kB] 318s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-decorator all 5.2.1-2 [28.1 kB] 318s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-scipy amd64 1.15.3-1 [16.6 MB] 318s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 318s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 319s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.5 kB] 319s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpython3.14-stdlib amd64 3.14.0-1 [2396 kB] 319s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3.14 amd64 3.14.0-1 [805 kB] 319s Get:111 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.13.7-2 [890 B] 319s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzopfli1 amd64 1.0.3-3 [141 kB] 319s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-zopfli amd64 0.2.3.post1-1 [10.8 kB] 319s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 319s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-fonttools amd64 4.57.0-1 [1497 kB] 319s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 319s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 319s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 319s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-matplotlib amd64 3.10.1+dfsg1-4 [18.0 MB] 319s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-3 [163 kB] 319s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-9 [4949 kB] 319s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 319s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 319s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-joblib all 1.4.2-4 [205 kB] 319s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 320s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 320s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyfaidx all 0.8.1.3-2 [29.7 kB] 320s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 320s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 320s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 320s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 320s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 320s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 320s Get:134 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu2 [178 kB] 320s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-28ubuntu7 [180 kB] 320s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 320s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 320s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 320s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu76 amd64 76.1-4ubuntu2 [11.2 MB] 320s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.15.0-2.3ubuntu1 [180 kB] 320s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 320s Get:142 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.13-4 [19.3 kB] 320s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 320s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.56.3-1build1 [247 kB] 320s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1build1 [55.0 kB] 320s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1build1 [30.3 kB] 320s Get:147 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 320s Get:148 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1 [16.4 kB] 320s Get:149 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 320s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.1-1 [28.9 MB] 320s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 321s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 321s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 321s Get:154 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-i686-linux-gnu-base amd64 15.2.0-4ubuntu4cross1 [58.1 kB] 321s Get:155 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-i686-linux-gnu amd64 15.2.0-4ubuntu4cross1 [13.7 MB] 321s Get:156 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [5730 B] 321s Get:157 http://ftpmaster.internal/ubuntu resolute/main amd64 binutils-i686-linux-gnu amd64 2.45-7ubuntu2 [1756 kB] 321s Get:158 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-cross-base all 15.2.0-4ubuntu4cross1 [53.2 kB] 321s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-i386-cross all 2.42-0ubuntu3cross1 [1582 kB] 321s Get:160 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1-i386-cross all 15.2.0-4ubuntu4cross1 [94.1 kB] 321s Get:161 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1-i386-cross all 15.2.0-4ubuntu4cross1 [152 kB] 321s Get:162 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1-i386-cross all 15.2.0-4ubuntu4cross1 [31.1 kB] 321s Get:163 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1-i386-cross all 15.2.0-4ubuntu4cross1 [8156 B] 321s Get:164 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8-i386-cross all 15.2.0-4ubuntu4cross1 [2906 kB] 321s Get:165 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6-i386-cross all 15.2.0-4ubuntu4cross1 [827 kB] 321s Get:166 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1-i386-cross all 15.2.0-4ubuntu4cross1 [1171 kB] 321s Get:167 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0-i386-cross all 15.2.0-4ubuntu4cross1 [245 kB] 322s Get:168 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev-i386-cross all 15.2.0-4ubuntu4cross1 [2755 kB] 322s Get:169 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-i686-linux-gnu amd64 15.2.0-4ubuntu4cross1 [27.0 MB] 322s Get:170 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [1220 B] 322s Get:171 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev-i386-cross all 6.17.0-4.4cross1 [1503 kB] 322s Get:172 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev-i386-cross all 2.42-0ubuntu3cross1 [1992 kB] 322s Get:173 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev-i386-cross all 15.2.0-4ubuntu4cross1 [2654 kB] 322s Get:174 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-i686-linux-gnu amd64 15.2.0-4ubuntu4cross1 [15.3 MB] 322s Get:175 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-i686-linux-gnu amd64 4:15.2.0-4ubuntu1 [954 B] 322s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 crossbuild-essential-i386 all 12.12ubuntu1 [3984 B] 322s Get:177 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.24.2ubuntu1 [95.7 kB] 322s Get:178 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-4build1 [169 kB] 322s Get:179 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 322s Get:180 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 322s Get:181 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.14.2-1 [20.4 kB] 322s Get:182 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.14.2-1 [5098 B] 322s Get:183 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 322s Get:184 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 322s Get:185 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.1-2build2 [1043 kB] 322s Get:186 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 322s Get:187 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 322s Get:188 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.24.2ubuntu1 [896 kB] 322s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 6.20250414 [119 kB] 322s Get:190 http://ftpmaster.internal/ubuntu resolute/universe i386 gcc-11-base i386 11.5.0-7ubuntu1 [46.4 kB] 322s Get:191 http://ftpmaster.internal/ubuntu resolute/universe i386 libasan6 i386 11.5.0-7ubuntu1 [2122 kB] 323s Get:192 http://ftpmaster.internal/ubuntu resolute/main i386 linux-libc-dev i386 6.17.0-5.5 [1813 kB] 323s Get:193 http://ftpmaster.internal/ubuntu resolute/main i386 libcrypt-dev i386 1:4.4.38-1build1 [121 kB] 323s Get:194 http://ftpmaster.internal/ubuntu resolute/main i386 libc6-dev i386 2.42-0ubuntu3 [1946 kB] 323s Get:195 http://ftpmaster.internal/ubuntu resolute/main i386 libgomp1 i386 15.2.0-5ubuntu1 [155 kB] 323s Get:196 http://ftpmaster.internal/ubuntu resolute/main i386 libitm1 i386 15.2.0-5ubuntu1 [31.6 kB] 323s Get:197 http://ftpmaster.internal/ubuntu resolute/main i386 libubsan1 i386 15.2.0-5ubuntu1 [1172 kB] 323s Get:198 http://ftpmaster.internal/ubuntu resolute/main i386 libquadmath0 i386 15.2.0-5ubuntu1 [246 kB] 323s Get:199 http://ftpmaster.internal/ubuntu resolute/universe i386 libgcc-11-dev i386 11.5.0-7ubuntu1 [2450 kB] 323s Get:200 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpgme11t64 amd64 1.24.2-3ubuntu1 [144 kB] 323s Get:201 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpgmepp6t64 amd64 1.24.2-3ubuntu1 [124 kB] 323s Get:202 http://ftpmaster.internal/ubuntu resolute/main amd64 libnspr4 amd64 2:4.36-1ubuntu2 [118 kB] 323s Get:203 http://ftpmaster.internal/ubuntu resolute/main amd64 libnss3 amd64 2:3.114-1 [1483 kB] 323s Get:204 http://ftpmaster.internal/ubuntu resolute/main amd64 libpoppler147 amd64 25.03.0-10 [1225 kB] 323s Get:205 http://ftpmaster.internal/ubuntu resolute/universe i386 libstdc++-11-dev i386 11.5.0-7ubuntu1 [2459 kB] 323s Get:206 http://ftpmaster.internal/ubuntu resolute/main amd64 poppler-utils amd64 25.03.0-10 [229 kB] 323s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 6.20250414 [1746 B] 323s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 323s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-wheel all 0.46.1-2 [22.1 kB] 323s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-build all 1.2.2-2 [31.0 kB] 323s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 323s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-pyproject all 6.20250414 [1728 B] 323s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 323s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 323s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 323s Preconfiguring packages ... 323s Fetched 362 MB in 9s (39.7 MB/s) 323s Selecting previously unselected package python3-numpy-dev:amd64. 323s (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 ... 78439 files and directories currently installed.) 323s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 323s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 323s Selecting previously unselected package libblas3:amd64. 323s Preparing to unpack .../001-libblas3_3.12.1-6build1_amd64.deb ... 323s Unpacking libblas3:amd64 (3.12.1-6build1) ... 323s Selecting previously unselected package libgfortran5:amd64. 323s Preparing to unpack .../002-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 323s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 323s Selecting previously unselected package liblapack3:amd64. 323s Preparing to unpack .../003-liblapack3_3.12.1-6build1_amd64.deb ... 323s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 323s Selecting previously unselected package python3-numpy. 323s Preparing to unpack .../004-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 323s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 323s Selecting previously unselected package libpython3.14-minimal:amd64. 323s Preparing to unpack .../005-libpython3.14-minimal_3.14.0-1_amd64.deb ... 323s Unpacking libpython3.14-minimal:amd64 (3.14.0-1) ... 323s Selecting previously unselected package python3.14-minimal. 323s Preparing to unpack .../006-python3.14-minimal_3.14.0-1_amd64.deb ... 323s Unpacking python3.14-minimal (3.14.0-1) ... 324s Selecting previously unselected package libcrypt1:i386. 324s Preparing to unpack .../007-libcrypt1_1%3a4.4.38-1build1_i386.deb ... 324s Unpacking libcrypt1:i386 (1:4.4.38-1build1) ... 324s Selecting previously unselected package libatomic1:i386. 324s Preparing to unpack .../008-libatomic1_15.2.0-5ubuntu1_i386.deb ... 324s Unpacking libatomic1:i386 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libstdc++6:i386. 324s Preparing to unpack .../009-libstdc++6_15.2.0-5ubuntu1_i386.deb ... 324s Unpacking libstdc++6:i386 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package m4. 324s Preparing to unpack .../010-m4_1.4.19-8_amd64.deb ... 324s Unpacking m4 (1.4.19-8) ... 324s Selecting previously unselected package autoconf. 324s Preparing to unpack .../011-autoconf_2.72-3.1ubuntu1_all.deb ... 324s Unpacking autoconf (2.72-3.1ubuntu1) ... 324s Selecting previously unselected package autotools-dev. 324s Preparing to unpack .../012-autotools-dev_20240727.1_all.deb ... 324s Unpacking autotools-dev (20240727.1) ... 324s Selecting previously unselected package automake. 324s Preparing to unpack .../013-automake_1%3a1.17-4ubuntu1_all.deb ... 324s Unpacking automake (1:1.17-4ubuntu1) ... 324s Selecting previously unselected package autopoint. 324s Preparing to unpack .../014-autopoint_0.23.1-2build2_all.deb ... 324s Unpacking autopoint (0.23.1-2build2) ... 324s Selecting previously unselected package libtcl8.6:amd64. 324s Preparing to unpack .../015-libtcl8.6_8.6.17+dfsg-1_amd64.deb ... 324s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1) ... 324s Selecting previously unselected package fonts-dejavu-mono. 324s Preparing to unpack .../016-fonts-dejavu-mono_2.37-8_all.deb ... 324s Unpacking fonts-dejavu-mono (2.37-8) ... 324s Selecting previously unselected package fonts-dejavu-core. 324s Preparing to unpack .../017-fonts-dejavu-core_2.37-8_all.deb ... 324s Unpacking fonts-dejavu-core (2.37-8) ... 324s Selecting previously unselected package libfontenc1:amd64. 324s Preparing to unpack .../018-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 324s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 324s Selecting previously unselected package x11-common. 324s Preparing to unpack .../019-x11-common_1%3a7.7+24ubuntu1_all.deb ... 324s Unpacking x11-common (1:7.7+24ubuntu1) ... 324s Selecting previously unselected package xfonts-encodings. 324s Preparing to unpack .../020-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 324s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 324s Selecting previously unselected package xfonts-utils. 324s Preparing to unpack .../021-xfonts-utils_1%3a7.7+7_amd64.deb ... 324s Unpacking xfonts-utils (1:7.7+7) ... 324s Selecting previously unselected package fonts-urw-base35. 324s Preparing to unpack .../022-fonts-urw-base35_20200910-8_all.deb ... 324s Unpacking fonts-urw-base35 (20200910-8) ... 324s Selecting previously unselected package fontconfig-config. 324s Preparing to unpack .../023-fontconfig-config_2.15.0-2.3ubuntu1_amd64.deb ... 324s Unpacking fontconfig-config (2.15.0-2.3ubuntu1) ... 324s Selecting previously unselected package libfontconfig1:amd64. 324s Preparing to unpack .../024-libfontconfig1_2.15.0-2.3ubuntu1_amd64.deb ... 324s Unpacking libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 324s Selecting previously unselected package libxrender1:amd64. 324s Preparing to unpack .../025-libxrender1_1%3a0.9.12-1_amd64.deb ... 324s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 324s Selecting previously unselected package libxft2:amd64. 324s Preparing to unpack .../026-libxft2_2.3.6-1build1_amd64.deb ... 324s Unpacking libxft2:amd64 (2.3.6-1build1) ... 324s Selecting previously unselected package libxss1:amd64. 324s Preparing to unpack .../027-libxss1_1%3a1.2.3-1build3_amd64.deb ... 324s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 324s Selecting previously unselected package libtk8.6:amd64. 324s Preparing to unpack .../028-libtk8.6_8.6.17-1_amd64.deb ... 324s Unpacking libtk8.6:amd64 (8.6.17-1) ... 324s Selecting previously unselected package tk8.6-blt2.5. 324s Preparing to unpack .../029-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 324s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 324s Selecting previously unselected package blt. 324s Preparing to unpack .../030-blt_2.5.3+dfsg-8_amd64.deb ... 324s Unpacking blt (2.5.3+dfsg-8) ... 324s Selecting previously unselected package libisl23:amd64. 324s Preparing to unpack .../031-libisl23_0.27-1_amd64.deb ... 324s Unpacking libisl23:amd64 (0.27-1) ... 324s Selecting previously unselected package libmpc3:amd64. 324s Preparing to unpack .../032-libmpc3_1.3.1-1build3_amd64.deb ... 324s Unpacking libmpc3:amd64 (1.3.1-1build3) ... 324s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 324s Preparing to unpack .../033-cpp-15-x86-64-linux-gnu_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package cpp-15. 324s Preparing to unpack .../034-cpp-15_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking cpp-15 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package cpp-x86-64-linux-gnu. 324s Preparing to unpack .../035-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 324s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 324s Selecting previously unselected package cpp. 324s Preparing to unpack .../036-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 324s Unpacking cpp (4:15.2.0-4ubuntu1) ... 324s Selecting previously unselected package libcc1-0:amd64. 324s Preparing to unpack .../037-libcc1-0_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libcc1-0:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libgomp1:amd64. 324s Preparing to unpack .../038-libgomp1_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libgomp1:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libitm1:amd64. 324s Preparing to unpack .../039-libitm1_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libitm1:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libasan8:amd64. 324s Preparing to unpack .../040-libasan8_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libasan8:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package liblsan0:amd64. 324s Preparing to unpack .../041-liblsan0_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking liblsan0:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libtsan2:amd64. 324s Preparing to unpack .../042-libtsan2_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libtsan2:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libubsan1:amd64. 324s Preparing to unpack .../043-libubsan1_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libubsan1:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libhwasan0:amd64. 324s Preparing to unpack .../044-libhwasan0_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libhwasan0:amd64 (15.2.0-5ubuntu1) ... 324s Selecting previously unselected package libquadmath0:amd64. 324s Preparing to unpack .../045-libquadmath0_15.2.0-5ubuntu1_amd64.deb ... 324s Unpacking libquadmath0:amd64 (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package libgcc-15-dev:amd64. 325s Preparing to unpack .../046-libgcc-15-dev_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking libgcc-15-dev:amd64 (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 325s Preparing to unpack .../047-gcc-15-x86-64-linux-gnu_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package gcc-15. 325s Preparing to unpack .../048-gcc-15_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking gcc-15 (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package gcc-x86-64-linux-gnu. 325s Preparing to unpack .../049-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 325s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 325s Selecting previously unselected package gcc. 325s Preparing to unpack .../050-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 325s Unpacking gcc (4:15.2.0-4ubuntu1) ... 325s Selecting previously unselected package libstdc++-15-dev:amd64. 325s Preparing to unpack .../051-libstdc++-15-dev_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking libstdc++-15-dev:amd64 (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package g++-15-x86-64-linux-gnu. 325s Preparing to unpack .../052-g++-15-x86-64-linux-gnu_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking g++-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package g++-15. 325s Preparing to unpack .../053-g++-15_15.2.0-5ubuntu1_amd64.deb ... 325s Unpacking g++-15 (15.2.0-5ubuntu1) ... 325s Selecting previously unselected package g++-x86-64-linux-gnu. 325s Preparing to unpack .../054-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 325s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 325s Selecting previously unselected package g++. 325s Preparing to unpack .../055-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 325s Unpacking g++ (4:15.2.0-4ubuntu1) ... 325s Selecting previously unselected package build-essential. 325s Preparing to unpack .../056-build-essential_12.12ubuntu1_amd64.deb ... 325s Unpacking build-essential (12.12ubuntu1) ... 325s Selecting previously unselected package python3-charset-normalizer. 325s Preparing to unpack .../057-python3-charset-normalizer_3.4.2-1_amd64.deb ... 325s Unpacking python3-charset-normalizer (3.4.2-1) ... 325s Selecting previously unselected package python3.13-tk. 325s Preparing to unpack .../058-python3.13-tk_3.13.7-1_amd64.deb ... 325s Unpacking python3.13-tk (3.13.7-1) ... 325s Selecting previously unselected package python3-tk:amd64. 325s Preparing to unpack .../059-python3-tk_3.13.5-1_amd64.deb ... 325s Unpacking python3-tk:amd64 (3.13.5-1) ... 325s Selecting previously unselected package python3-pil.imagetk:amd64. 325s Preparing to unpack .../060-python3-pil.imagetk_11.3.0-1ubuntu1_amd64.deb ... 325s Unpacking python3-pil.imagetk:amd64 (11.3.0-1ubuntu1) ... 325s Selecting previously unselected package libimagequant0:amd64. 325s Preparing to unpack .../061-libimagequant0_2.18.0-1build1_amd64.deb ... 325s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 325s Selecting previously unselected package libjpeg-turbo8:amd64. 325s Preparing to unpack .../062-libjpeg-turbo8_2.1.5-4ubuntu2_amd64.deb ... 325s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 325s Selecting previously unselected package libjpeg8:amd64. 325s Preparing to unpack .../063-libjpeg8_8c-2ubuntu11_amd64.deb ... 325s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 325s Selecting previously unselected package liblcms2-2:amd64. 325s Preparing to unpack .../064-liblcms2-2_2.16-2_amd64.deb ... 325s Unpacking liblcms2-2:amd64 (2.16-2) ... 325s Selecting previously unselected package libopenjp2-7:amd64. 325s Preparing to unpack .../065-libopenjp2-7_2.5.3-2.1_amd64.deb ... 325s Unpacking libopenjp2-7:amd64 (2.5.3-2.1) ... 325s Selecting previously unselected package libgraphite2-3:amd64. 325s Preparing to unpack .../066-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 325s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 325s Selecting previously unselected package libharfbuzz0b:amd64. 325s Preparing to unpack .../067-libharfbuzz0b_10.2.0-1_amd64.deb ... 325s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 325s Selecting previously unselected package libraqm0:amd64. 325s Preparing to unpack .../068-libraqm0_0.10.3-1_amd64.deb ... 325s Unpacking libraqm0:amd64 (0.10.3-1) ... 325s Selecting previously unselected package libdeflate0:amd64. 325s Preparing to unpack .../069-libdeflate0_1.23-2_amd64.deb ... 325s Unpacking libdeflate0:amd64 (1.23-2) ... 325s Selecting previously unselected package libjbig0:amd64. 325s Preparing to unpack .../070-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 325s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 325s Selecting previously unselected package liblerc4:amd64. 325s Preparing to unpack .../071-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 325s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 325s Selecting previously unselected package libsharpyuv0:amd64. 325s Preparing to unpack .../072-libsharpyuv0_1.5.0-0.1_amd64.deb ... 325s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 325s Selecting previously unselected package libwebp7:amd64. 325s Preparing to unpack .../073-libwebp7_1.5.0-0.1_amd64.deb ... 325s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 325s Selecting previously unselected package libtiff6:amd64. 325s Preparing to unpack .../074-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 325s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 325s Selecting previously unselected package libwebpdemux2:amd64. 325s Preparing to unpack .../075-libwebpdemux2_1.5.0-0.1_amd64.deb ... 325s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 325s Selecting previously unselected package libwebpmux3:amd64. 325s Preparing to unpack .../076-libwebpmux3_1.5.0-0.1_amd64.deb ... 325s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 325s Selecting previously unselected package python3-pil:amd64. 325s Preparing to unpack .../077-python3-pil_11.3.0-1ubuntu1_amd64.deb ... 325s Unpacking python3-pil:amd64 (11.3.0-1ubuntu1) ... 325s Selecting previously unselected package libpixman-1-0:amd64. 325s Preparing to unpack .../078-libpixman-1-0_0.44.0-3_amd64.deb ... 325s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 325s Selecting previously unselected package libxcb-render0:amd64. 325s Preparing to unpack .../079-libxcb-render0_1.17.0-2build1_amd64.deb ... 325s Unpacking libxcb-render0:amd64 (1.17.0-2build1) ... 325s Selecting previously unselected package libxcb-shm0:amd64. 325s Preparing to unpack .../080-libxcb-shm0_1.17.0-2build1_amd64.deb ... 325s Unpacking libxcb-shm0:amd64 (1.17.0-2build1) ... 325s Selecting previously unselected package libcairo2:amd64. 325s Preparing to unpack .../081-libcairo2_1.18.4-1build1_amd64.deb ... 325s Unpacking libcairo2:amd64 (1.18.4-1build1) ... 325s 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previously unselected package python3-scipy. 326s Preparing to unpack .../104-python3-scipy_1.15.3-1_amd64.deb ... 326s Unpacking python3-scipy (1.15.3-1) ... 326s Selecting previously unselected package python3-mpmath. 326s Preparing to unpack .../105-python3-mpmath_1.3.0-1_all.deb ... 326s Unpacking python3-mpmath (1.3.0-1) ... 326s Selecting previously unselected package python3-sympy. 326s Preparing to unpack .../106-python3-sympy_1.13.3-5_all.deb ... 326s Unpacking python3-sympy (1.13.3-5) ... 326s Selecting previously unselected package python3-ufolib2. 326s Preparing to unpack .../107-python3-ufolib2_0.17.1+dfsg1-1_all.deb ... 326s Unpacking python3-ufolib2 (0.17.1+dfsg1-1) ... 326s Selecting previously unselected package libpython3.14-stdlib:amd64. 326s Preparing to unpack .../108-libpython3.14-stdlib_3.14.0-1_amd64.deb ... 326s Unpacking libpython3.14-stdlib:amd64 (3.14.0-1) ... 326s Selecting previously unselected package python3.14. 326s Preparing to unpack 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python3-kiwisolver. 326s Preparing to unpack .../115-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 326s Unpacking python3-kiwisolver (1.4.7-3build1) ... 326s Selecting previously unselected package python3-packaging. 326s Preparing to unpack .../116-python3-packaging_25.0-1_all.deb ... 326s Unpacking python3-packaging (25.0-1) ... 326s Selecting previously unselected package libqhull-r8.0:amd64. 326s Preparing to unpack .../117-libqhull-r8.0_2020.2-6build1_amd64.deb ... 326s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 326s Selecting previously unselected package python3-matplotlib. 326s Preparing to unpack .../118-python3-matplotlib_3.10.1+dfsg1-4_amd64.deb ... 326s Unpacking python3-matplotlib (3.10.1+dfsg1-4) ... 327s Selecting previously unselected package python3-pytz. 327s Preparing to unpack .../119-python3-pytz_2025.2-3_all.deb ... 327s Unpacking python3-pytz (2025.2-3) ... 327s Selecting previously unselected package python3-pandas-lib:amd64. 327s Preparing to unpack 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Unpacking python3-pomegranate (0.15.0-1build1) ... 327s Selecting previously unselected package python3-pyfaidx. 327s Preparing to unpack .../126-python3-pyfaidx_0.8.1.3-2_all.deb ... 327s Unpacking python3-pyfaidx (0.8.1.3-2) ... 327s Selecting previously unselected package libhtscodecs2:amd64. 327s Preparing to unpack .../127-libhtscodecs2_1.6.1-2_amd64.deb ... 327s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 327s Selecting previously unselected package libhts3t64:amd64. 327s Preparing to unpack .../128-libhts3t64_1.21+ds-1_amd64.deb ... 327s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 327s Selecting previously unselected package python3-pysam. 327s Preparing to unpack .../129-python3-pysam_0.23.0+ds-1build1_amd64.deb ... 327s Unpacking python3-pysam (0.23.0+ds-1build1) ... 327s Selecting previously unselected package python3-threadpoolctl. 327s Preparing to unpack .../130-python3-threadpoolctl_3.1.0-1_all.deb ... 327s Unpacking python3-threadpoolctl (3.1.0-1) ... 327s Selecting previously unselected package python3-sklearn-lib:amd64. 327s Preparing to unpack .../131-python3-sklearn-lib_1.4.2+dfsg-8_amd64.deb ... 327s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 328s Selecting previously unselected package python3-sklearn. 328s Preparing to unpack .../132-python3-sklearn_1.4.2+dfsg-8_all.deb ... 328s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 328s Selecting previously unselected package zip. 328s Preparing to unpack .../133-zip_3.0-15ubuntu2_amd64.deb ... 328s Unpacking zip (3.0-15ubuntu2) ... 328s Selecting previously unselected package unzip. 328s Preparing to unpack .../134-unzip_6.0-28ubuntu7_amd64.deb ... 328s Unpacking unzip (6.0-28ubuntu7) ... 328s Selecting previously unselected package libpaper2:amd64. 328s Preparing to unpack .../135-libpaper2_2.2.5-0.3_amd64.deb ... 328s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 328s Selecting previously unselected package libpaper-utils. 328s Preparing to unpack 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Selecting previously unselected package libthai0:amd64. 328s Preparing to unpack .../142-libthai0_0.1.29-2build1_amd64.deb ... 328s Unpacking libthai0:amd64 (0.1.29-2build1) ... 328s Selecting previously unselected package libpango-1.0-0:amd64. 328s Preparing to unpack .../143-libpango-1.0-0_1.56.3-1build1_amd64.deb ... 328s Unpacking libpango-1.0-0:amd64 (1.56.3-1build1) ... 328s Selecting previously unselected package libpangoft2-1.0-0:amd64. 328s Preparing to unpack .../144-libpangoft2-1.0-0_1.56.3-1build1_amd64.deb ... 328s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-1build1) ... 328s Selecting previously unselected package libpangocairo-1.0-0:amd64. 328s Preparing to unpack .../145-libpangocairo-1.0-0_1.56.3-1build1_amd64.deb ... 328s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-1build1) ... 328s Selecting previously unselected package libice6:amd64. 328s Preparing to unpack .../146-libice6_2%3a1.1.1-1_amd64.deb ... 328s Unpacking libice6:amd64 (2:1.1.1-1) ... 328s Selecting previously unselected package libsm6:amd64. 328s Preparing to unpack .../147-libsm6_2%3a1.2.6-1_amd64.deb ... 328s Unpacking libsm6:amd64 (2:1.2.6-1) ... 328s Selecting previously unselected package libxt6t64:amd64. 328s Preparing to unpack .../148-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 328s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 328s Selecting previously unselected package r-base-core. 328s Preparing to unpack .../149-r-base-core_4.5.1-1_amd64.deb ... 328s Unpacking r-base-core (4.5.1-1) ... 328s Selecting previously unselected package r-bioc-biocgenerics. 328s Preparing to unpack .../150-r-bioc-biocgenerics_0.52.0-2_all.deb ... 328s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 328s Selecting previously unselected package r-bioc-dnacopy. 328s Preparing to unpack .../151-r-bioc-dnacopy_1.80.0-2_amd64.deb ... 328s Unpacking r-bioc-dnacopy (1.80.0-2) ... 328s Selecting previously unselected package cnvkit. 328s Preparing to unpack .../152-cnvkit_0.9.12-1_all.deb ... 328s Unpacking cnvkit (0.9.12-1) ... 328s Selecting previously unselected package gcc-15-i686-linux-gnu-base:amd64. 328s Preparing to unpack .../153-gcc-15-i686-linux-gnu-base_15.2.0-4ubuntu4cross1_amd64.deb ... 328s Unpacking gcc-15-i686-linux-gnu-base:amd64 (15.2.0-4ubuntu4cross1) ... 328s Selecting previously unselected package cpp-15-i686-linux-gnu. 328s Preparing to unpack .../154-cpp-15-i686-linux-gnu_15.2.0-4ubuntu4cross1_amd64.deb ... 328s Unpacking cpp-15-i686-linux-gnu (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package cpp-i686-linux-gnu. 329s Preparing to unpack .../155-cpp-i686-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 329s Unpacking cpp-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 329s Selecting previously unselected package binutils-i686-linux-gnu. 329s Preparing to unpack .../156-binutils-i686-linux-gnu_2.45-7ubuntu2_amd64.deb ... 329s Unpacking binutils-i686-linux-gnu (2.45-7ubuntu2) ... 329s Selecting previously unselected package gcc-15-cross-base. 329s Preparing to unpack .../157-gcc-15-cross-base_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking gcc-15-cross-base (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libc6-i386-cross. 329s Preparing to unpack .../158-libc6-i386-cross_2.42-0ubuntu3cross1_all.deb ... 329s Unpacking libc6-i386-cross (2.42-0ubuntu3cross1) ... 329s Selecting previously unselected package libgcc-s1-i386-cross. 329s Preparing to unpack .../159-libgcc-s1-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libgcc-s1-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libgomp1-i386-cross. 329s Preparing to unpack .../160-libgomp1-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libgomp1-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libitm1-i386-cross. 329s Preparing to unpack .../161-libitm1-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libitm1-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libatomic1-i386-cross. 329s Preparing to unpack .../162-libatomic1-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libatomic1-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libasan8-i386-cross. 329s Preparing to unpack .../163-libasan8-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libasan8-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libstdc++6-i386-cross. 329s Preparing to unpack .../164-libstdc++6-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libstdc++6-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libubsan1-i386-cross. 329s Preparing to unpack .../165-libubsan1-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libubsan1-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package libquadmath0-i386-cross. 329s Preparing to unpack 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(6.17.0-4.4cross1) ... 329s Selecting previously unselected package libc6-dev-i386-cross. 329s Preparing to unpack .../171-libc6-dev-i386-cross_2.42-0ubuntu3cross1_all.deb ... 329s Unpacking libc6-dev-i386-cross (2.42-0ubuntu3cross1) ... 329s Selecting previously unselected package libstdc++-15-dev-i386-cross. 329s Preparing to unpack .../172-libstdc++-15-dev-i386-cross_15.2.0-4ubuntu4cross1_all.deb ... 329s Unpacking libstdc++-15-dev-i386-cross (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package g++-15-i686-linux-gnu. 329s Preparing to unpack .../173-g++-15-i686-linux-gnu_15.2.0-4ubuntu4cross1_amd64.deb ... 329s Unpacking g++-15-i686-linux-gnu (15.2.0-4ubuntu4cross1) ... 329s Selecting previously unselected package g++-i686-linux-gnu. 329s Preparing to unpack .../174-g++-i686-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 329s Unpacking g++-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 329s Selecting previously unselected package crossbuild-essential-i386. 329s Preparing to unpack .../175-crossbuild-essential-i386_12.12ubuntu1_all.deb ... 329s Unpacking crossbuild-essential-i386 (12.12ubuntu1) ... 329s Selecting previously unselected package libdebhelper-perl. 329s Preparing to unpack .../176-libdebhelper-perl_13.24.2ubuntu1_all.deb ... 329s Unpacking libdebhelper-perl (13.24.2ubuntu1) ... 329s Selecting previously unselected package libtool. 329s Preparing to unpack .../177-libtool_2.5.4-4build1_all.deb ... 329s Unpacking libtool (2.5.4-4build1) ... 329s Selecting previously unselected package dh-autoreconf. 329s Preparing to unpack .../178-dh-autoreconf_21_all.deb ... 329s Unpacking dh-autoreconf (21) ... 330s Selecting previously unselected package libarchive-zip-perl. 330s Preparing to unpack .../179-libarchive-zip-perl_1.68-1_all.deb ... 330s Unpacking libarchive-zip-perl (1.68-1) ... 330s Selecting previously unselected package libfile-stripnondeterminism-perl. 330s Preparing to unpack .../180-libfile-stripnondeterminism-perl_1.14.2-1_all.deb ... 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python3-iniconfig (1.1.1-2) ... 330s Selecting previously unselected package python3-pluggy. 330s Preparing to unpack .../213-python3-pluggy_1.5.0-1_all.deb ... 330s Unpacking python3-pluggy (1.5.0-1) ... 330s Selecting previously unselected package python3-pytest. 330s Preparing to unpack .../214-python3-pytest_8.3.5-2_all.deb ... 330s Unpacking python3-pytest (8.3.5-2) ... 330s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 330s Setting up dh-python (6.20250414) ... 331s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 331s Setting up liblcms2-2:amd64 (2.16-2) ... 331s Setting up python3-iniconfig (1.1.1-2) ... 331s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 331s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 331s Setting up gcc-11-base:i386 (11.5.0-7ubuntu1) ... 331s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 331s Setting up libxrender1:amd64 (1:0.9.12-1) ... 331s Setting up libdatrie1:amd64 (0.2.13-4) ... 331s Setting up python3-joblib (1.4.2-4) ... 331s Setting up 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332s Setting up python3-freetype (2.5.1-1) ... 332s Setting up python3-networkx (3.2.1-4ubuntu1) ... 333s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 333s Setting up python3-platformdirs (4.3.7-1) ... 333s Setting up libasan6:i386 (11.5.0-7ubuntu1) ... 333s Setting up python3-fs (2.4.16-7) ... 334s Setting up unicode-data (15.1.0-1) ... 334s Setting up python3-decorator (5.2.1-2) ... 334s Setting up zip (3.0-15ubuntu2) ... 334s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 334s Setting up linux-libc-dev-i386-cross (6.17.0-4.4cross1) ... 334s Setting up autotools-dev (20240727.1) ... 334s Setting up libblas3:amd64 (3.12.1-6build1) ... 334s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 334s Setting up python3-packaging (25.0-1) ... 334s Setting up python3-pyproject-hooks (1.2.0-1) ... 334s Setting up libzopfli1 (1.0.3-3) ... 334s Setting up libnspr4:amd64 (2:4.36-1ubuntu2) ... 334s Setting up python3-brotli (1.1.0-2build5) ... 334s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 334s Setting up libquadmath0:amd64 (15.2.0-5ubuntu1) ... 334s Setting up libquadmath0:i386 (15.2.0-5ubuntu1) ... 334s Setting up python3-cycler (0.12.1-1) ... 334s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 334s Setting up fonts-dejavu-mono (2.37-8) ... 334s Setting up python3-kiwisolver (1.4.7-3build1) ... 334s Setting up libmpc3:amd64 (1.3.1-1build3) ... 334s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 334s Setting up libatomic1:i386 (15.2.0-5ubuntu1) ... 334s Setting up gcc-15-i686-linux-gnu-base:amd64 (15.2.0-4ubuntu4cross1) ... 334s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 335s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... 335s Setting up autopoint (0.23.1-2build2) ... 335s Setting up fonts-dejavu-core (2.37-8) ... 335s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu2) ... 335s Setting up python3-installer (0.7.0+dfsg1-3) ... 335s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 335s Setting up autoconf (2.72-3.1ubuntu1) ... 335s Setting up python3-pluggy (1.5.0-1) ... 335s /usr/lib/python3/dist-packages/pluggy/_callers.py:141: SyntaxWarning: 'return' in a 'finally' block 335s return result 335s /usr/lib/python3/dist-packages/pluggy/_callers.py:182: SyntaxWarning: 'return' in a 'finally' block 335s return outcome.get_result() 335s Setting up libwebp7:amd64 (1.5.0-0.1) ... 335s Setting up libubsan1:amd64 (15.2.0-5ubuntu1) ... 335s Setting up dwz (0.16-2) ... 335s Setting up libhwasan0:amd64 (15.2.0-5ubuntu1) ... 335s Setting up libcrypt-dev:i386 (1:4.4.38-1build1) ... 335s Setting up libasan8:amd64 (15.2.0-5ubuntu1) ... 335s Setting up libxslt1.1:amd64 (1.1.43-0.1) ... 335s Setting up debugedit (1:5.2-3) ... 335s Setting up libc6-i386-cross (2.42-0ubuntu3cross1) ... 335s Setting up libhts3t64:amd64 (1.21+ds-1) ... 335s Setting up libopenjp2-7:amd64 (2.5.3-2.1) ... 335s Setting up libc6-dev:i386 (2.42-0ubuntu3) ... 335s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 335s Setting up libthai-data (0.1.29-2build1) ... 335s Setting up python3-dateutil (2.9.0-4) ... 335s Setting up sgml-base (1.31+nmu1) ... 336s Setting up libgpgme11t64:amd64 (1.24.2-3ubuntu1) ... 336s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 336s Setting up libicu76:amd64 (76.1-4ubuntu2) ... 336s Setting up libpaper2:amd64 (2.2.5-0.3) ... 336s Setting up libtsan2:amd64 (15.2.0-5ubuntu1) ... 336s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 336s Setting up python3-mpmath (1.3.0-1) ... 336s Setting up libisl23:amd64 (0.27-1) ... 336s Setting up gcc-15-cross-base (15.2.0-4ubuntu4cross1) ... 336s Setting up python-matplotlib-data (3.10.1+dfsg1-4) ... 336s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 336s Setting up libquadmath0-i386-cross (15.2.0-4ubuntu4cross1) ... 336s Setting up xdg-utils (1.2.1-2ubuntu1) ... 336s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 336s Setting up python3.14-minimal (3.14.0-1) ... 337s Setting up libcc1-0:amd64 (15.2.0-5ubuntu1) ... 337s Setting up libstdc++6:i386 (15.2.0-5ubuntu1) ... 337s Setting up liblsan0:amd64 (15.2.0-5ubuntu1) ... 337s Setting up libitm1:amd64 (15.2.0-5ubuntu1) ... 337s Setting up libitm1:i386 (15.2.0-5ubuntu1) ... 337s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 337s Setting up automake (1:1.17-4ubuntu1) ... 337s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 337s Setting up libfile-stripnondeterminism-perl (1.14.2-1) ... 337s Setting up python3-pyfaidx (0.8.1.3-2) ... 337s Setting up python3-sympy (1.13.3-5) ... 343s /usr/lib/python3/dist-packages/sympy/testing/runtests.py:282: SyntaxWarning: 'return' in a 'finally' block 343s return p.returncode 344s Setting up libgpgmepp6t64:amd64 (1.24.2-3ubuntu1) ... 344s Setting up libice6:amd64 (2:1.1.1-1) ... 344s Setting up liblapack3:amd64 (3.12.1-6build1) ... 344s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 344s Setting up gettext (0.23.1-2build2) ... 344s Setting up python3-pysam (0.23.0+ds-1build1) ... 344s Setting up libgcc-15-dev:amd64 (15.2.0-5ubuntu1) ... 344s Setting up libatomic1-i386-cross (15.2.0-4ubuntu4cross1) ... 344s Setting up libpython3.14-stdlib:amd64 (3.14.0-1) ... 344s Setting up fontconfig-config (2.15.0-2.3ubuntu1) ... 344s Setting up python3-pytest (8.3.5-2) ... 344s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 344s Setting up cpp-15-i686-linux-gnu (15.2.0-4ubuntu4cross1) ... 344s Setting up libnss3:amd64 (2:3.114-1) ... 344s Setting up libgomp1-i386-cross (15.2.0-4ubuntu4cross1) ... 344s Setting up libc6-dev-i386-cross (2.42-0ubuntu3cross1) ... 344s Setting up libpaper-utils (2.2.5-0.3) ... 344s Setting up cpp-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 344s Setting up xfonts-utils (1:7.7+7) ... 344s Setting up python3-wheel (0.46.1-2) ... 344s Setting up python3-zopfli (0.2.3.post1-1) ... 344s Setting up intltool-debian (0.35.0+20060710.6) ... 344s Setting up gcc-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 344s Setting up libgcc-s1-i386-cross (15.2.0-4ubuntu4cross1) ... 344s Setting up libthai0:amd64 (0.1.29-2build1) ... 344s Setting up libstdc++-15-dev:amd64 (15.2.0-5ubuntu1) ... 344s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 344s Setting up libraqm0:amd64 (0.10.3-1) ... 344s Setting up libitm1-i386-cross (15.2.0-4ubuntu4cross1) ... 344s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 346s Setting up libubsan1:i386 (15.2.0-5ubuntu1) ... 346s Setting up dh-strip-nondeterminism (1.14.2-1) ... 346s Setting up libgcc-11-dev:i386 (11.5.0-7ubuntu1) ... 346s Setting up cpp-15 (15.2.0-5ubuntu1) ... 346s Setting up python3-lxml:amd64 (6.0.1-1) ... 347s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ... 347s Setting up xml-core (0.19) ... 347s Setting up python3-contourpy (1.3.1-1build1) ... 347s Setting up cpp-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 347s Setting up libfontconfig1:amd64 (2.15.0-2.3ubuntu1) ... 347s Setting up python3.14 (3.14.0-1) ... 347s Setting up python3-build (1.2.2-2) ... 348s Setting up libsm6:amd64 (2:1.2.6-1) ... 348s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 348s Setting up g++-15-x86-64-linux-gnu (15.2.0-5ubuntu1) ... 348s Setting up fontconfig (2.15.0-2.3ubuntu1) ... 350s Regenerating fonts cache... done. 350s Setting up libxft2:amd64 (2.3.6-1build1) ... 350s Setting up python3-scipy (1.15.3-1) ... 352s /usr/lib/python3/dist-packages/scipy/optimize/_optimize.py:921: SyntaxWarning: 'break' in a 'finally' block 352s break 354s Setting up libpoppler147:amd64 (25.03.0-10) ... 354s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 354s Setting up pybuild-plugin-pyproject (6.20250414) ... 354s Setting up po-debconf (1.0.21+nmu1) ... 354s Setting up python3-pomegranate (0.15.0-1build1) ... 354s Setting up libtk8.6:amd64 (8.6.17-1) ... 354s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-9) ... 354s Setting up libpango-1.0-0:amd64 (1.56.3-1build1) ... 354s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 354s Setting up python3-all (3.13.7-2) ... 354s Setting up fonts-urw-base35 (20200910-8) ... 354s Setting up libcairo2:amd64 (1.18.4-1build1) ... 354s Setting up python3.13-tk (3.13.7-1) ... 354s Setting up libasan8-i386-cross (15.2.0-4ubuntu4cross1) ... 354s Setting up libstdc++6-i386-cross (15.2.0-4ubuntu4cross1) ... 354s Setting up python3-pil:amd64 (11.3.0-1ubuntu1) ... 354s Setting up gcc-15 (15.2.0-5ubuntu1) ... 354s Setting up python3-pandas (2.2.3+dfsg-9) ... 360s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 360s Setting up python3-sklearn (1.4.2+dfsg-8) ... 362s Setting up libstdc++-11-dev:i386 (11.5.0-7ubuntu1) ... 362s Setting up cpp (4:15.2.0-4ubuntu1) ... 362s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 362s Setting up poppler-utils (25.03.0-10) ... 362s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1build1) ... 362s Setting up g++-15 (15.2.0-5ubuntu1) ... 362s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1build1) ... 362s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 362s Setting up python3-cairo (1.27.0-2) ... 362s Setting up libtool (2.5.4-4build1) ... 362s Setting up blt (2.5.3+dfsg-8) ... 362s Setting up python3-tk:amd64 (3.13.5-1) ... 362s Setting up libubsan1-i386-cross (15.2.0-4ubuntu4cross1) ... 362s Setting up gcc (4:15.2.0-4ubuntu1) ... 362s Setting up dh-autoreconf (21) ... 362s Setting up libgcc-15-dev-i386-cross (15.2.0-4ubuntu4cross1) ... 362s Setting up python3-pil.imagetk:amd64 (11.3.0-1ubuntu1) ... 362s Setting up python3-rlpycairo (0.3.0-3) ... 362s Setting up r-base-core (4.5.1-1) ... 362s Creating config file /etc/R/Renviron with new version 362s Setting up python3-reportlab (4.4.2-1) ... 363s Setting up libstdc++-15-dev-i386-cross (15.2.0-4ubuntu4cross1) ... 363s Setting up g++ (4:15.2.0-4ubuntu1) ... 363s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 363s Setting up build-essential (12.12ubuntu1) ... 363s Setting up r-bioc-biocgenerics (0.52.0-2) ... 363s Setting up gcc-15-i686-linux-gnu (15.2.0-4ubuntu4cross1) ... 363s Setting up debhelper (13.24.2ubuntu1) ... 363s Setting up g++-15-i686-linux-gnu (15.2.0-4ubuntu4cross1) ... 363s Setting up r-bioc-dnacopy (1.80.0-2) ... 363s Setting up gcc-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 363s Setting up g++-i686-linux-gnu (4:15.2.0-4ubuntu1) ... 363s Setting up pybuild-plugin-autopkgtest (6.20250414) ... 363s Setting up crossbuild-essential-i386 (12.12ubuntu1) ... 363s Setting up python3-fonttools (4.57.0-1) ... 364s Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... 364s Setting up python3-matplotlib (3.10.1+dfsg1-4) ... 366s Processing triggers for libc-bin (2.42-0ubuntu3) ... 366s Processing triggers for systemd (257.9-0ubuntu2) ... 366s Processing triggers for man-db (2.13.1-1) ... 367s Processing triggers for install-info (7.1.1-1ubuntu1) ... 367s Processing triggers for sgml-base (1.31+nmu1) ... 367s Setting up w3c-sgml-lib (1.3-3) ... 383s Setting up python3-biopython (1.85+dfsg-4) ... 384s Setting up cnvkit (0.9.12-1) ... 387s autopkgtest [15:59:52]: test environment configured for cross building 387s autopkgtest [15:59:52]: test pybuild-autopkgtest: pybuild-autopkgtest 387s autopkgtest [15:59:52]: test pybuild-autopkgtest: [----------------------- 388s pybuild-autopkgtest 388s I: pybuild base:311: cd /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build; python3.14 -m pytest test 388s ============================= test session starts ============================== 388s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.5.0 388s rootdir: /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build 388s configfile: pyproject.toml 388s plugins: typeguard-4.4.2 388s collected 0 items / 5 errors 388s 388s ==================================== ERRORS ==================================== 388s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 388s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_cnvlib.py'. 388s Hint: make sure your test modules/packages have valid Python names. 388s Traceback: 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 388s from . import multiarray 388s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 388s from . import overrides 388s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 388s from numpy._core._multiarray_umath import ( 388s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 388s 388s During handling of the above exception, another exception occurred: 388s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 388s from numpy.__config__ import show_config 388s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 388s from numpy._core._multiarray_umath import ( 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 388s raise ImportError(msg) 388s E ImportError: 388s E 388s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 388s E 388s E Importing the numpy C-extensions failed. This error can happen for 388s E many reasons, often due to issues with your setup or how NumPy was 388s E installed. 388s E 388s E We have compiled some common reasons and troubleshooting tips at: 388s E 388s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 388s E 388s E Please note and check the following: 388s E 388s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 388s E * The NumPy version is: "2.2.4" 388s E 388s E and make sure that they are the versions you expect. 388s E Please carefully study the documentation linked above for further help. 388s E 388s E Original error was: No module named 'numpy._core._multiarray_umath' 388s 388s The above exception was the direct cause of the following exception: 388s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 388s return _bootstrap._gcd_import(name[level:], package, level) 388s test/test_cnvlib.py:14: in 388s import numpy as np 388s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 388s raise ImportError(msg) from e 388s E ImportError: Error importing numpy: you should not try to import numpy from 388s E its source directory; please exit the numpy source tree, and relaunch 388s E your python interpreter from there. 388s ____________________ ERROR collecting test/test_commands.py ____________________ 388s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_commands.py'. 388s Hint: make sure your test modules/packages have valid Python names. 388s Traceback: 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 388s from . import multiarray 388s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 388s from . import overrides 388s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 388s from numpy._core._multiarray_umath import ( 388s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 388s 388s During handling of the above exception, another exception occurred: 388s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 388s from numpy.__config__ import show_config 388s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 388s from numpy._core._multiarray_umath import ( 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 388s raise ImportError(msg) 388s E ImportError: 388s E 388s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 388s E 388s E Importing the numpy C-extensions failed. This error can happen for 388s E many reasons, often due to issues with your setup or how NumPy was 388s E installed. 388s E 388s E We have compiled some common reasons and troubleshooting tips at: 388s E 388s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 388s E 388s E Please note and check the following: 388s E 388s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 388s E * The NumPy version is: "2.2.4" 388s E 388s E and make sure that they are the versions you expect. 388s E Please carefully study the documentation linked above for further help. 388s E 388s E Original error was: No module named 'numpy._core._multiarray_umath' 388s 388s The above exception was the direct cause of the following exception: 388s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 388s return _bootstrap._gcd_import(name[level:], package, level) 388s test/test_commands.py:18: in 388s import numpy as np 388s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 388s raise ImportError(msg) from e 388s E ImportError: Error importing numpy: you should not try to import numpy from 388s E its source directory; please exit the numpy source tree, and relaunch 388s E your python interpreter from there. 388s _____________________ ERROR collecting test/test_genome.py _____________________ 388s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_genome.py'. 388s Hint: make sure your test modules/packages have valid Python names. 388s Traceback: 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 388s from . import multiarray 388s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 388s from . import overrides 388s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 388s from numpy._core._multiarray_umath import ( 388s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 388s 388s During handling of the above exception, another exception occurred: 388s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 388s from numpy.__config__ import show_config 388s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 388s from numpy._core._multiarray_umath import ( 388s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 388s raise ImportError(msg) 388s E ImportError: 388s E 388s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 388s E 388s E Importing the numpy C-extensions failed. This error can happen for 388s E many reasons, often due to issues with your setup or how NumPy was 388s E installed. 388s E 388s E We have compiled some common reasons and troubleshooting tips at: 388s E 388s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 388s E 388s E Please note and check the following: 388s E 388s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 388s E * The NumPy version is: "2.2.4" 388s E 388s E and make sure that they are the versions you expect. 388s E Please carefully study the documentation linked above for further help. 388s E 388s E Original error was: No module named 'numpy._core._multiarray_umath' 388s 388s The above exception was the direct cause of the following exception: 388s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 388s return _bootstrap._gcd_import(name[level:], package, level) 388s test/test_genome.py:12: in 388s import numpy as np 388s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 388s raise ImportError(msg) from e 388s E ImportError: Error importing numpy: you should not try to import numpy from 388s E its source directory; please exit the numpy source tree, and relaunch 388s E your python interpreter from there. 388s _______________________ ERROR collecting test/test_io.py _______________________ 388s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_io.py'. 388s Hint: make sure your test modules/packages have valid Python names. 388s Traceback: 388s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 388s return _bootstrap._gcd_import(name[level:], package, level) 388s test/test_io.py:11: in 388s from skgenome import tabio 388s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 388s from . import tabio 388s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 388s import pandas as pd 388s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 388s raise ImportError( 388s E ImportError: Unable to import required dependencies: 388s E numpy: Error importing numpy: you should not try to import numpy from 388s E its source directory; please exit the numpy source tree, and relaunch 388s E your python interpreter from there. 388s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 388s _______________________ ERROR collecting test/test_r.py ________________________ 388s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_r.py'. 388s Hint: make sure your test modules/packages have valid Python names. 388s Traceback: 388s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 388s return _bootstrap._gcd_import(name[level:], package, level) 388s test/test_r.py:14: in 388s import cnvlib 388s /usr/lib/python3/dist-packages/cnvlib/__init__.py:1: in 388s from skgenome.tabio import write 388s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 388s from . import tabio 388s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 388s import pandas as pd 388s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 388s raise ImportError( 388s E ImportError: Unable to import required dependencies: 388s E numpy: Error importing numpy: you should not try to import numpy from 388s E its source directory; please exit the numpy source tree, and relaunch 388s E your python interpreter from there. 388s =========================== short test summary info ============================ 388s ERROR test/test_cnvlib.py 388s ERROR test/test_commands.py 388s ERROR test/test_genome.py 388s ERROR test/test_io.py 388s ERROR test/test_r.py 388s !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! 388s ============================== 5 errors in 0.13s =============================== 388s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build; python3.14 -m pytest test 388s I: pybuild base:311: cd /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build; python3.13 -m pytest test 389s ============================= test session starts ============================== 389s platform linux -- Python 3.13.7, pytest-8.3.5, pluggy-1.5.0 389s rootdir: /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build 389s configfile: pyproject.toml 389s plugins: typeguard-4.4.2 389s collected 10 items / 4 errors 389s 389s ==================================== ERRORS ==================================== 389s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 389s ImportError while importing test module '/tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build/test/test_cnvlib.py'. 389s Hint: make sure your test modules/packages have valid Python names. 389s Traceback: 389s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 389s return _bootstrap._gcd_import(name[level:], package, level) 389s test/test_cnvlib.py:15: in 389s from skgenome import GenomicArray, tabio 389s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 389s from . import tabio 389s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 389s import pandas as pd 389s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 389s raise ImportError( 389s E ImportError: Unable to import required dependencies: 389s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 389s ____________________ ERROR collecting test/test_commands.py ____________________ 389s test/test_commands.py:21: in 389s import cnvlib 389s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 389s from .cmdutil import read_cna as read 389s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 389s from .cnary import CopyNumArray as CNA 389s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 389s from scipy.stats import median_test 389s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 389s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 389s E TypeError: can only concatenate str (not "NoneType") to str 389s _____________________ ERROR collecting test/test_genome.py _____________________ 389s test/test_genome.py:15: in 389s from cnvlib import read_ga 389s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 389s from .cmdutil import read_cna as read 389s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 389s from .cnary import CopyNumArray as CNA 389s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 389s from scipy.stats import median_test 389s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 389s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 389s E TypeError: can only concatenate str (not "NoneType") to str 389s _______________________ ERROR collecting test/test_r.py ________________________ 389s test/test_r.py:14: in 389s import cnvlib 389s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 389s from .cmdutil import read_cna as read 389s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 389s from .cnary import CopyNumArray as CNA 389s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 389s from scipy.stats import median_test 389s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 389s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 389s E TypeError: can only concatenate str (not "NoneType") to str 389s =========================== short test summary info ============================ 389s ERROR test/test_cnvlib.py 389s ERROR test/test_commands.py - TypeError: can only concatenate str (not "NoneT... 389s ERROR test/test_genome.py - TypeError: can only concatenate str (not "NoneTyp... 389s ERROR test/test_r.py - TypeError: can only concatenate str (not "NoneType") t... 389s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 389s ============================== 4 errors in 0.30s =============================== 389s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.Uu4CYm/autopkgtest_tmp/build; python3.13 -m pytest test 389s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 389s make: *** [/tmp/IxFixfI6QP/run:4: pybuild-autopkgtest] Error 25 389s pybuild-autopkgtest: error: /tmp/IxFixfI6QP/run pybuild-autopkgtest returned exit code 2 389s autopkgtest [15:59:54]: test pybuild-autopkgtest: -----------------------] 389s pybuild-autopkgtest FAIL non-zero exit status 25 389s autopkgtest [15:59:54]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 390s autopkgtest [15:59:55]: @@@@@@@@@@@@@@@@@@@@ summary 390s run-unit-test PASS 390s pybuild-autopkgtest FAIL non-zero exit status 25