0s autopkgtest [08:54:21]: starting date and time: 2024-11-13 08:54:21+0000 0s autopkgtest [08:54:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:54:21]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pfnsxkkp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-20.secgroup --name adt-plucky-arm64-cnvkit-20241113-085421-juju-7f2275-prod-proposed-migration-environment-15-6d1967ba-0d00-475c-b084-f692800b121d --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 75s autopkgtest [08:55:36]: testbed dpkg architecture: arm64 75s autopkgtest [08:55:36]: testbed apt version: 2.9.8 75s autopkgtest [08:55:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 77s Fetched 1793 kB in 1s (1998 kB/s) 77s Reading package lists... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 83s The following NEW packages will be installed: 83s python3.13-gdbm 83s The following packages will be upgraded: 83s libpython3-stdlib python3 python3-gdbm python3-minimal 83s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 101 kB of archives. 83s After this operation, 141 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 83s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 83s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 84s Fetched 101 kB in 0s (269 kB/s) 84s (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 ... 79924 files and directories currently installed.) 84s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 84s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 84s Setting up python3-minimal (3.12.7-1) ... 85s (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 ... 79924 files and directories currently installed.) 85s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 85s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 85s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 85s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 85s Selecting previously unselected package python3.13-gdbm. 85s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 85s Unpacking python3.13-gdbm (3.13.0-2) ... 85s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 85s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 85s Setting up python3.13-gdbm (3.13.0-2) ... 85s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 85s Setting up python3 (3.12.7-1) ... 86s Setting up python3-gdbm:arm64 (3.12.7-1) ... 86s Processing triggers for man-db (2.12.1-3) ... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 89s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 89s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 90s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s Calculating upgrade... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s autopkgtest [08:55:59]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 98s autopkgtest [08:55:59]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (dsc) [2449 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (tar) [23.7 MB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (diff) [17.7 kB] 104s gpgv: Signature made Mon Apr 8 08:42:55 2024 UTC 104s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found 105s autopkgtest [08:56:06]: testing package cnvkit version 0.9.10-2 105s autopkgtest [08:56:06]: build not needed 109s autopkgtest [08:56:10]: test run-unit-test: preparing testbed 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 114s The following additional packages will be installed: 114s blt cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 114s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 libdeflate0 114s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 114s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 114s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 114s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 114s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 114s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 114s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 114s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 114s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 114s python3-cairo python3-contourpy python3-cycler python3-dateutil 114s python3-decorator python3-fonttools python3-freetype python3-fs 114s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 114s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 114s python3-packaging python3-pandas python3-pandas-lib python3-pil 114s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 114s python3-reportlab python3-rlpycairo python3-scipy python3-six 114s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 114s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 114s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 114s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 114s xfonts-encodings xfonts-utils xml-core zip 114s Suggested packages: 114s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 114s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 114s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 114s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 114s t-coffee wise python-cycler-doc python-joblib-doc python-lxml-doc 114s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 114s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 114s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 114s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 114s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 114s python3-dev python3-pytest python-pandas-doc python3-statsmodels 114s python-pil-doc python-pomegranate-doc pdf-viewer python3-egenix-mxtexttools 114s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 114s python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 114s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase 114s r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray 114s r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy 114s r-bioc-deseq2 r-bioc-annotate r-cran-runit sgml-base-doc debhelper 114s Recommended packages: 114s javascript-common poppler-data python-biopython-doc ncbi-blast+ 114s python3-pytest python3-simplejson python3-psutil python3-bs4 114s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 114s python3-odf python3-openpyxl python3-tables python3-olefile 114s fonts-dejavu-extra g++ | c++-compiler isympy-common r-recommended r-base-dev 114s r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 114s x11-utils x11-xserver-utils 114s The following NEW packages will be installed: 114s autopkgtest-satdep blt cnvkit fontconfig fontconfig-config fonts-dejavu-core 114s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 114s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 114s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 114s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 114s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 114s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 114s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 114s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 114s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 114s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 114s python3-cairo python3-contourpy python3-cycler python3-dateutil 114s python3-decorator python3-fonttools python3-freetype python3-fs 114s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 114s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 114s python3-packaging python3-pandas python3-pandas-lib python3-pil 114s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 114s python3-reportlab python3-rlpycairo python3-scipy python3-six 114s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 114s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 114s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 114s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 114s xfonts-encodings xfonts-utils xml-core zip 114s 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 156 MB/156 MB of archives. 114s After this operation, 661 MB of additional disk space will be used. 114s Get:1 /tmp/autopkgtest.DAZmaz/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [987 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 115s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 115s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 115s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 115s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 115s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 115s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 115s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 115s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 115s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 115s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 115s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.15-1 [774 kB] 116s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 116s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 116s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 116s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 116s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 116s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 116s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.12-tk arm64 3.12.7-3 [115 kB] 116s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-tk arm64 3.13.0-2 [105 kB] 116s Get:25 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-tk arm64 3.12.7-1 [9752 B] 116s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pil.imagetk arm64 10.4.0-1ubuntu1 [9504 B] 116s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 116s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 116s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] 116s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 116s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 116s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu1 [182 kB] 116s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 116s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.0.1-1 [487 kB] 116s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 116s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 116s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 116s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] 116s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [16.3 kB] 116s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.4.0-0.1 [192 kB] 116s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 116s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 116s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 116s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 10.4.0-1ubuntu1 [456 kB] 116s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 116s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 116s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 116s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 116s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2 [121 kB] 116s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 116s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 116s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.2.5-1 [1107 kB] 116s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 116s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 116s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.84+dfsg-4 [1689 kB] 116s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 116s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 116s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-lyx all 2.4.2.1-1 [171 kB] 116s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-matplotlib-data all 3.8.3-3 [2928 kB] 116s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 116s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 116s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-contourpy arm64 1.3.0-2 [179 kB] 116s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 116s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 116s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 116s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 116s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 117s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 117s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 117s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sympy all 1.13.3-1 [4228 kB] 117s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 117s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 117s Get:73 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 117s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libxslt1.1 arm64 1.1.39-0exp1ubuntu1 [167 kB] 117s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lxml arm64 5.3.0-1 [1205 kB] 117s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 117s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 117s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 117s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 117s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-kiwisolver arm64 1.4.7-2 [50.4 kB] 117s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 117s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 117s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-matplotlib arm64 3.8.3-3 [4515 kB] 117s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 118s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 118s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 118s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 118s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pomegranate arm64 0.14.8-6 [2432 kB] 118s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 118s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 118s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 118s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 118s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pysam arm64 0.22.1+ds-2 [3412 kB] 118s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 118s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 118s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 118s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu1 [172 kB] 118s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 118s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] 118s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 1.1.29build1 [8490 B] 118s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 118s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-1.1ubuntu2 [190 kB] 118s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 119s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 119s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 119s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.54.0+ds-3 [234 kB] 119s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-3 [48.9 kB] 119s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-3 [27.5 kB] 119s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 119s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 119s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 119s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1 [28.4 MB] 120s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.50.0-2 [605 kB] 120s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-dnacopy arm64 1.78.0-1 [377 kB] 120s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 cnvkit all 0.9.10-2 [20.5 MB] 121s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libpoppler140 arm64 24.08.0-1 [1111 kB] 121s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 poppler-utils arm64 24.08.0-1 [212 kB] 121s Preconfiguring packages ... 122s Fetched 156 MB in 7s (22.2 MB/s) 122s Selecting previously unselected package sgml-base. 122s (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 ... 79931 files and directories currently installed.) 122s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 122s Unpacking sgml-base (1.31) ... 122s Selecting previously unselected package libtcl8.6:arm64. 122s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_arm64.deb ... 122s Unpacking libtcl8.6:arm64 (8.6.15+dfsg-2) ... 122s Selecting previously unselected package fonts-dejavu-mono. 122s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-mono (2.37-8) ... 122s Selecting previously unselected package fonts-dejavu-core. 122s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 122s Unpacking fonts-dejavu-core (2.37-8) ... 122s Selecting previously unselected package libfontenc1:arm64. 122s Preparing to unpack .../004-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 122s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 122s Selecting previously unselected package x11-common. 122s Preparing to unpack .../005-x11-common_1%3a7.7+23ubuntu3_all.deb ... 122s Unpacking x11-common (1:7.7+23ubuntu3) ... 122s Selecting previously unselected package xfonts-encodings. 122s Preparing to unpack .../006-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 122s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 122s Selecting previously unselected package xfonts-utils. 122s Preparing to unpack .../007-xfonts-utils_1%3a7.7+7_arm64.deb ... 122s Unpacking xfonts-utils (1:7.7+7) ... 122s Selecting previously unselected package fonts-urw-base35. 122s Preparing to unpack .../008-fonts-urw-base35_20200910-8_all.deb ... 123s Unpacking fonts-urw-base35 (20200910-8) ... 123s Selecting previously unselected package fontconfig-config. 123s Preparing to unpack .../009-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 123s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 123s Selecting previously unselected package libfontconfig1:arm64. 123s Preparing to unpack .../010-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 123s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 123s Selecting previously unselected package libxrender1:arm64. 124s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 124s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 124s Selecting previously unselected package libxft2:arm64. 124s Preparing to unpack .../012-libxft2_2.3.6-1build1_arm64.deb ... 124s Unpacking libxft2:arm64 (2.3.6-1build1) ... 124s Selecting previously unselected package libxss1:arm64. 124s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_arm64.deb ... 124s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 124s Selecting previously unselected package libtk8.6:arm64. 124s Preparing to unpack .../014-libtk8.6_8.6.15-1_arm64.deb ... 124s Unpacking libtk8.6:arm64 (8.6.15-1) ... 124s Selecting previously unselected package tk8.6-blt2.5. 124s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 124s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 124s Selecting previously unselected package blt. 124s Preparing to unpack .../016-blt_2.5.3+dfsg-7build1_arm64.deb ... 124s Unpacking blt (2.5.3+dfsg-7build1) ... 124s Selecting previously unselected package libblas3:arm64. 124s Preparing to unpack .../017-libblas3_3.12.0-3build2_arm64.deb ... 124s Unpacking libblas3:arm64 (3.12.0-3build2) ... 124s Selecting previously unselected package libgfortran5:arm64. 124s Preparing to unpack .../018-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 124s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 124s Selecting previously unselected package liblapack3:arm64. 124s Preparing to unpack .../019-liblapack3_3.12.0-3build2_arm64.deb ... 124s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 124s Selecting previously unselected package python3-numpy. 124s Preparing to unpack .../020-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 124s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 125s Selecting previously unselected package python3.12-tk. 125s Preparing to unpack .../021-python3.12-tk_3.12.7-3_arm64.deb ... 125s Unpacking python3.12-tk (3.12.7-3) ... 125s Selecting previously unselected package python3.13-tk. 125s Preparing to unpack .../022-python3.13-tk_3.13.0-2_arm64.deb ... 125s Unpacking python3.13-tk (3.13.0-2) ... 125s Selecting previously unselected package python3-tk:arm64. 125s Preparing to unpack .../023-python3-tk_3.12.7-1_arm64.deb ... 125s Unpacking python3-tk:arm64 (3.12.7-1) ... 125s Selecting previously unselected package python3-pil.imagetk:arm64. 125s Preparing to unpack .../024-python3-pil.imagetk_10.4.0-1ubuntu1_arm64.deb ... 125s Unpacking python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 125s Selecting previously unselected package libgomp1:arm64. 125s Preparing to unpack .../025-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 125s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 125s Selecting previously unselected package libimagequant0:arm64. 125s Preparing to unpack .../026-libimagequant0_2.18.0-1build1_arm64.deb ... 125s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 125s Selecting previously unselected package libjpeg-turbo8:arm64. 125s Preparing to unpack .../027-libjpeg-turbo8_2.1.5-2ubuntu2_arm64.deb ... 125s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 125s Selecting previously unselected package libjpeg8:arm64. 125s Preparing to unpack .../028-libjpeg8_8c-2ubuntu11_arm64.deb ... 125s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 125s Selecting previously unselected package liblcms2-2:arm64. 125s Preparing to unpack .../029-liblcms2-2_2.16-2_arm64.deb ... 125s Unpacking liblcms2-2:arm64 (2.16-2) ... 125s Selecting previously unselected package libopenjp2-7:arm64. 125s Preparing to unpack .../030-libopenjp2-7_2.5.0-2ubuntu1_arm64.deb ... 125s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 125s Selecting previously unselected package libgraphite2-3:arm64. 125s Preparing to unpack .../031-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 125s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 125s Selecting previously unselected package libharfbuzz0b:arm64. 125s Preparing to unpack .../032-libharfbuzz0b_10.0.1-1_arm64.deb ... 125s Unpacking libharfbuzz0b:arm64 (10.0.1-1) ... 125s Selecting previously unselected package libraqm0:arm64. 125s Preparing to unpack .../033-libraqm0_0.10.1-1build1_arm64.deb ... 125s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 125s Selecting previously unselected package libdeflate0:arm64. 125s Preparing to unpack .../034-libdeflate0_1.22-1_arm64.deb ... 125s Unpacking libdeflate0:arm64 (1.22-1) ... 125s Selecting previously unselected package libjbig0:arm64. 125s Preparing to unpack .../035-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 125s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 125s Selecting previously unselected package liblerc4:arm64. 125s Preparing to unpack .../036-liblerc4_4.0.0+ds-4ubuntu2_arm64.deb ... 125s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 125s Selecting previously unselected package libsharpyuv0:arm64. 126s Preparing to unpack .../037-libsharpyuv0_1.4.0-0.1_arm64.deb ... 126s Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... 126s Selecting previously unselected package libwebp7:arm64. 126s Preparing to unpack .../038-libwebp7_1.4.0-0.1_arm64.deb ... 126s Unpacking libwebp7:arm64 (1.4.0-0.1) ... 126s Selecting previously unselected package libtiff6:arm64. 126s Preparing to unpack .../039-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 126s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 126s Selecting previously unselected package libwebpdemux2:arm64. 126s Preparing to unpack .../040-libwebpdemux2_1.4.0-0.1_arm64.deb ... 126s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 126s Selecting previously unselected package libwebpmux3:arm64. 126s Preparing to unpack .../041-libwebpmux3_1.4.0-0.1_arm64.deb ... 126s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 126s Selecting previously unselected package python3-pil:arm64. 126s Preparing to unpack .../042-python3-pil_10.4.0-1ubuntu1_arm64.deb ... 126s Unpacking python3-pil:arm64 (10.4.0-1ubuntu1) ... 126s Selecting previously unselected package libpixman-1-0:arm64. 126s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_arm64.deb ... 126s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 126s Selecting previously unselected package libxcb-render0:arm64. 126s Preparing to unpack .../044-libxcb-render0_1.17.0-2_arm64.deb ... 126s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 126s Selecting previously unselected package libxcb-shm0:arm64. 126s Preparing to unpack .../045-libxcb-shm0_1.17.0-2_arm64.deb ... 126s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 126s Selecting previously unselected package libcairo2:arm64. 126s Preparing to unpack .../046-libcairo2_1.18.2-2_arm64.deb ... 126s Unpacking libcairo2:arm64 (1.18.2-2) ... 126s Selecting previously unselected package python3-cairo. 126s Preparing to unpack .../047-python3-cairo_1.26.1-2_arm64.deb ... 126s Unpacking python3-cairo (1.26.1-2) ... 126s Selecting previously unselected package python3-freetype. 126s Preparing to unpack .../048-python3-freetype_2.5.1-1_all.deb ... 126s Unpacking python3-freetype (2.5.1-1) ... 126s Selecting previously unselected package python3-rlpycairo. 126s Preparing to unpack .../049-python3-rlpycairo_0.3.0-3_all.deb ... 126s Unpacking python3-rlpycairo (0.3.0-3) ... 126s Selecting previously unselected package python3-reportlab. 126s Preparing to unpack .../050-python3-reportlab_4.2.5-1_all.deb ... 126s Unpacking python3-reportlab (4.2.5-1) ... 127s Selecting previously unselected package xml-core. 127s Preparing to unpack .../051-xml-core_0.19_all.deb ... 127s Unpacking xml-core (0.19) ... 127s Selecting previously unselected package w3c-sgml-lib. 127s Preparing to unpack .../052-w3c-sgml-lib_1.3-3_all.deb ... 127s Unpacking w3c-sgml-lib (1.3-3) ... 127s Selecting previously unselected package python3-biopython. 127s Preparing to unpack .../053-python3-biopython_1.84+dfsg-4_arm64.deb ... 127s Unpacking python3-biopython (1.84+dfsg-4) ... 127s Selecting previously unselected package libjs-jquery. 127s Preparing to unpack .../054-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 127s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 127s Selecting previously unselected package libjs-jquery-ui. 127s Preparing to unpack .../055-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 127s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 127s Selecting previously unselected package fonts-lyx. 127s Preparing to unpack .../056-fonts-lyx_2.4.2.1-1_all.deb ... 127s Unpacking fonts-lyx (2.4.2.1-1) ... 127s Selecting previously unselected package python-matplotlib-data. 127s Preparing to unpack .../057-python-matplotlib-data_3.8.3-3_all.deb ... 127s Unpacking python-matplotlib-data (3.8.3-3) ... 127s Selecting previously unselected package python3-six. 127s Preparing to unpack .../058-python3-six_1.16.0-7_all.deb ... 127s Unpacking python3-six (1.16.0-7) ... 127s Selecting previously unselected package python3-dateutil. 127s Preparing to unpack .../059-python3-dateutil_2.9.0-2_all.deb ... 127s Unpacking python3-dateutil (2.9.0-2) ... 127s Selecting previously unselected package python3-contourpy. 127s Preparing to unpack .../060-python3-contourpy_1.3.0-2_arm64.deb ... 127s Unpacking python3-contourpy (1.3.0-2) ... 127s Selecting previously unselected package python3-cycler. 127s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 127s Unpacking python3-cycler (0.12.1-1) ... 127s Selecting previously unselected package python3-brotli. 128s Preparing to unpack .../062-python3-brotli_1.1.0-2build2_arm64.deb ... 128s Unpacking python3-brotli (1.1.0-2build2) ... 128s Selecting previously unselected package python3-decorator. 128s Preparing to unpack .../063-python3-decorator_5.1.1-5_all.deb ... 128s Unpacking python3-decorator (5.1.1-5) ... 128s Selecting previously unselected package liblbfgsb0:arm64. 128s Preparing to unpack .../064-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 128s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 128s Selecting previously unselected package python3-scipy. 128s Preparing to unpack .../065-python3-scipy_1.13.1-5_arm64.deb ... 128s Unpacking python3-scipy (1.13.1-5) ... 128s Selecting previously unselected package python3-ufolib2. 128s Preparing to unpack .../066-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 128s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 128s Selecting previously unselected package python3-mpmath. 128s Preparing to unpack .../067-python3-mpmath_1.3.0-1_all.deb ... 128s Unpacking python3-mpmath (1.3.0-1) ... 129s Selecting previously unselected package python3-sympy. 129s Preparing to unpack .../068-python3-sympy_1.13.3-1_all.deb ... 129s Unpacking python3-sympy (1.13.3-1) ... 129s Selecting previously unselected package python3-tz. 129s Preparing to unpack .../069-python3-tz_2024.1-2_all.deb ... 129s Unpacking python3-tz (2024.1-2) ... 129s Selecting previously unselected package python3-appdirs. 129s Preparing to unpack .../070-python3-appdirs_1.4.4-4_all.deb ... 129s Unpacking python3-appdirs (1.4.4-4) ... 129s Selecting previously unselected package python3-fs. 129s Preparing to unpack .../071-python3-fs_2.4.16-4_all.deb ... 129s Unpacking python3-fs (2.4.16-4) ... 129s Selecting previously unselected package libxslt1.1:arm64. 129s Preparing to unpack .../072-libxslt1.1_1.1.39-0exp1ubuntu1_arm64.deb ... 129s Unpacking libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 129s Selecting previously unselected package python3-lxml:arm64. 129s Preparing to unpack .../073-python3-lxml_5.3.0-1_arm64.deb ... 129s Unpacking python3-lxml:arm64 (5.3.0-1) ... 129s Selecting previously unselected package python3-lz4. 129s Preparing to unpack .../074-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 129s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 129s Selecting previously unselected package python3-unicodedata2. 129s Preparing to unpack .../075-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 129s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 129s Selecting previously unselected package unicode-data. 129s Preparing to unpack .../076-unicode-data_15.1.0-1_all.deb ... 129s Unpacking unicode-data (15.1.0-1) ... 130s Selecting previously unselected package python3-fonttools. 130s Preparing to unpack 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python3-threadpoolctl (3.1.0-1) ... 133s Selecting previously unselected package python3-sklearn-lib:arm64. 133s Preparing to unpack .../093-python3-sklearn-lib_1.4.2+dfsg-6_arm64.deb ... 133s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 133s Selecting previously unselected package python3-sklearn. 133s Preparing to unpack .../094-python3-sklearn_1.4.2+dfsg-6_all.deb ... 133s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 133s Selecting previously unselected package zip. 133s Preparing to unpack .../095-zip_3.0-14ubuntu1_arm64.deb ... 133s Unpacking zip (3.0-14ubuntu1) ... 133s Selecting previously unselected package unzip. 133s Preparing to unpack .../096-unzip_6.0-28ubuntu6_arm64.deb ... 133s Unpacking unzip (6.0-28ubuntu6) ... 133s Selecting previously unselected package libpaper1:arm64. 133s Preparing to unpack .../097-libpaper1_1.1.29build1_arm64.deb ... 133s Unpacking libpaper1:arm64 (1.1.29build1) ... 133s Selecting previously unselected package libpaper-utils. 133s 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libthai0:arm64 (0.1.29-2build1) ... 134s Selecting previously unselected package libpango-1.0-0:arm64. 134s Preparing to unpack .../104-libpango-1.0-0_1.54.0+ds-3_arm64.deb ... 134s Unpacking libpango-1.0-0:arm64 (1.54.0+ds-3) ... 134s Selecting previously unselected package libpangoft2-1.0-0:arm64. 134s Preparing to unpack .../105-libpangoft2-1.0-0_1.54.0+ds-3_arm64.deb ... 134s Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... 134s Selecting previously unselected package libpangocairo-1.0-0:arm64. 134s Preparing to unpack .../106-libpangocairo-1.0-0_1.54.0+ds-3_arm64.deb ... 134s Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... 134s Selecting previously unselected package libice6:arm64. 134s Preparing to unpack .../107-libice6_2%3a1.1.1-1_arm64.deb ... 134s Unpacking libice6:arm64 (2:1.1.1-1) ... 134s Selecting previously unselected package libsm6:arm64. 134s Preparing to unpack .../108-libsm6_2%3a1.2.4-1_arm64.deb ... 134s Unpacking libsm6:arm64 (2:1.2.4-1) ... 134s Selecting previously unselected package libxt6t64:arm64. 134s Preparing to unpack .../109-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 134s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 134s Selecting previously unselected package r-base-core. 134s Preparing to unpack .../110-r-base-core_4.4.2-1_arm64.deb ... 134s Unpacking r-base-core (4.4.2-1) ... 135s Selecting previously unselected package r-bioc-biocgenerics. 135s Preparing to unpack .../111-r-bioc-biocgenerics_0.50.0-2_all.deb ... 135s Unpacking r-bioc-biocgenerics (0.50.0-2) ... 135s Selecting previously unselected package r-bioc-dnacopy. 135s Preparing to unpack .../112-r-bioc-dnacopy_1.78.0-1_arm64.deb ... 135s Unpacking r-bioc-dnacopy (1.78.0-1) ... 135s Selecting previously unselected package cnvkit. 135s Preparing to unpack .../113-cnvkit_0.9.10-2_all.deb ... 135s Unpacking cnvkit (0.9.10-2) ... 136s Selecting previously unselected package libpoppler140:arm64. 136s Preparing to unpack .../114-libpoppler140_24.08.0-1_arm64.deb ... 136s Unpacking libpoppler140:arm64 (24.08.0-1) ... 136s Selecting previously unselected package poppler-utils. 136s Preparing to unpack .../115-poppler-utils_24.08.0-1_arm64.deb ... 136s Unpacking poppler-utils (24.08.0-1) ... 136s Selecting previously unselected package autopkgtest-satdep. 136s Preparing to unpack .../116-1-autopkgtest-satdep.deb ... 136s Unpacking autopkgtest-satdep (0) ... 136s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 136s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 136s Setting up liblcms2-2:arm64 (2.16-2) ... 136s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 136s Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... 136s Setting up libpaper1:arm64 (1.1.29build1) ... 136s 136s Creating config file /etc/papersize with new version 136s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu2) ... 136s Setting up python3-importlib-metadata (8.5.0-1) ... 136s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 136s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 136s Setting up python3-joblib (1.3.2-5) ... 137s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 137s Setting up libxcb-render0:arm64 (1.17.0-2) ... 137s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 137s Setting up fonts-lyx (2.4.2.1-1) ... 137s Setting up unzip (6.0-28ubuntu6) ... 137s Setting up python3-threadpoolctl (3.1.0-1) ... 137s Setting up x11-common (1:7.7+23ubuntu3) ... 137s Setting up libdeflate0:arm64 (1.22-1) ... 137s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 137s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 138s Setting up libpaper-utils (1.1.29build1) ... 138s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 138s Setting up python3-freetype (2.5.1-1) ... 138s Setting up python3-networkx (3.2.1-4ubuntu1) ... 140s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 140s Setting up python3-tz (2024.1-2) ... 140s Setting up unicode-data (15.1.0-1) ... 140s Setting up python3-six (1.16.0-7) ... 140s Setting up python3-decorator (5.1.1-5) ... 141s Setting up zip (3.0-14ubuntu1) ... 141s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 141s Setting up libblas3:arm64 (3.12.0-3build2) ... 141s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 141s Setting up python3-packaging (24.1-1) ... 141s Setting up python3-brotli (1.1.0-2build2) ... 141s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 141s Setting up python3-cycler (0.12.1-1) ... 141s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 141s Setting up fonts-dejavu-mono (2.37-8) ... 141s Setting up python3-kiwisolver (1.4.7-2) ... 141s Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... 141s Setting up fonts-dejavu-core (2.37-8) ... 141s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... 141s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 141s Setting up libwebp7:arm64 (1.4.0-0.1) ... 141s Setting up libxslt1.1:arm64 (1.1.39-0exp1ubuntu1) ... 141s Setting up libhts3t64:arm64 (1.20+ds-1) ... 141s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu1) ... 141s Setting up libharfbuzz0b:arm64 (10.0.1-1) ... 141s Setting up libthai-data (0.1.29-2build1) ... 141s Setting up python3-dateutil (2.9.0-2) ... 142s Setting up sgml-base (1.31) ... 142s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 142s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 142s Setting up python3-mpmath (1.3.0-1) ... 143s Setting up python-matplotlib-data (3.8.3-3) ... 143s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 143s Setting up python3-appdirs (1.4.4-4) ... 143s Setting up xdg-utils (1.2.1-0ubuntu1) ... 143s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 143s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 143s Setting up python3-pyfaidx (0.8.1.3-1) ... 143s Setting up python3-sympy (1.13.3-1) ... 152s Setting up libice6:arm64 (2:1.1.1-1) ... 152s Setting up liblapack3:arm64 (3.12.0-3build2) ... 152s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 152s Setting up python3-pysam (0.22.1+ds-2) ... 152s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 152s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 152s Setting up xfonts-utils (1:7.7+7) ... 152s Setting up python3-fs (2.4.16-4) ... 153s Setting up libthai0:arm64 (0.1.29-2build1) ... 153s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 153s Setting up libraqm0:arm64 (0.10.1-1build1) ... 153s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 155s Setting up python3-lxml:arm64 (5.3.0-1) ... 155s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 155s Setting up xml-core (0.19) ... 156s Setting up python3-contourpy (1.3.0-2) ... 156s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 156s Setting up libsm6:arm64 (2:1.2.4-1) ... 156s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 156s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 158s Regenerating fonts cache... done. 158s Setting up libxft2:arm64 (2.3.6-1build1) ... 158s Setting up python3-scipy (1.13.1-5) ... 162s Setting up python3-pomegranate (0.14.8-6) ... 162s Setting up libtk8.6:arm64 (8.6.15-1) ... 162s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 162s Setting up libpango-1.0-0:arm64 (1.54.0+ds-3) ... 162s Setting up python3.12-tk (3.12.7-3) ... 162s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 162s Setting up fonts-urw-base35 (20200910-8) ... 163s Setting up libcairo2:arm64 (1.18.2-2) ... 163s Setting up python3.13-tk (3.13.0-2) ... 163s Setting up python3-pil:arm64 (10.4.0-1ubuntu1) ... 163s Setting up python3-pandas (2.2.3+dfsg-5) ... 169s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 169s Setting up python3-sklearn (1.4.2+dfsg-6) ... 172s Setting up libpoppler140:arm64 (24.08.0-1) ... 172s Setting up poppler-utils (24.08.0-1) ... 172s Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-3) ... 172s Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-3) ... 172s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 172s Setting up python3-cairo (1.26.1-2) ... 172s Setting up blt (2.5.3+dfsg-7build1) ... 172s Setting up python3-tk:arm64 (3.12.7-1) ... 172s Setting up python3-pil.imagetk:arm64 (10.4.0-1ubuntu1) ... 172s Setting up python3-rlpycairo (0.3.0-3) ... 172s Setting up r-base-core (4.4.2-1) ... 172s 172s Creating config file /etc/R/Renviron with new version 172s Setting up python3-reportlab (4.2.5-1) ... 173s Setting up r-bioc-biocgenerics (0.50.0-2) ... 173s Setting up r-bioc-dnacopy (1.78.0-1) ... 173s Setting up python3-fonttools (4.46.0-1build2) ... 174s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 175s Setting up python3-matplotlib (3.8.3-3) ... 176s Processing triggers for libc-bin (2.40-1ubuntu3) ... 176s Processing triggers for man-db (2.12.1-3) ... 178s Processing triggers for install-info (7.1.1-1) ... 178s Processing triggers for sgml-base (1.31) ... 178s Setting up w3c-sgml-lib (1.3-3) ... 207s Setting up python3-biopython (1.84+dfsg-4) ... 208s Setting up cnvkit (0.9.10-2) ... 208s Setting up autopkgtest-satdep (0) ... 214s (Reading database ... 97150 files and directories currently installed.) 214s Removing autopkgtest-satdep (0) ... 215s autopkgtest [08:57:56]: test run-unit-test: [----------------------- 215s 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/ 218s Created directory build/ 218s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 218s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 218s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 218s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 218s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 218s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 218s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 218s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 218s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 219s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 220s Number of target and antitarget files: 3, 3 220s No FASTA reference genome provided; skipping GC, RM calculations 220s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 220s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 221s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 221s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 221s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 221s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 221s Loading build/p2-20_5.targetcoverage.cnn 221s Correcting for GC bias... 221s Correcting for density bias... 221s Loading build/p2-5_5.targetcoverage.cnn 221s Correcting for GC bias... 221s Correcting for density bias... 221s Loading build/p2-9_5.targetcoverage.cnn 221s Correcting for GC bias... 221s Correcting for density bias... 221s Loading build/p2-20_5.antitargetcoverage.cnn 221s Correcting for GC bias... 221s Loading build/p2-5_5.antitargetcoverage.cnn 221s Correcting for GC bias... 221s Loading build/p2-9_5.antitargetcoverage.cnn 221s Correcting for GC bias... 222s Calculating average bin coverages 228s Calculating bin spreads 229s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 229s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 229s " chr1:2435319-2436685 log2=-0.709 spread=0.503 229s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 229s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 229s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 229s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 229s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 229s " chr1:120611883-120612051 log2=0.070 spread=0.050 229s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 229s " chr1:156842391-156842479 log2=-0.398 spread=0.290 229s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 229s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 229s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 229s " chr1:183481886-183481951 log2=-0.040 spread=0.119 229s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 229s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 229s " chr1:243800859-243801066 log2=0.023 spread=0.063 229s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 229s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 229s " chr2:25536716-25536891 log2=0.702 spread=0.033 229s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 229s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 229s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 229s REL chr2:61108881-61109061 log2=1.026 spread=0.559 229s " chr2:61128072-61128256 log2=0.115 spread=0.173 229s " chr2:61145275-61145462 log2=0.014 spread=0.099 229s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 229s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 229s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 229s " chr2:128095237-128095425 log2=0.215 spread=0.212 229s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 229s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 229s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 229s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 229s " chr3:97160189-97160367 log2=-0.050 spread=0.191 229s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 229s " chr3:142286854-142287031 log2=-0.076 spread=0.116 229s GAK chr4:896278-896357 log2=-1.505 spread=1.261 229s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 229s " chr4:1803044-1803507 log2=-0.073 spread=0.117 229s " chr4:1808792-1809022 log2=0.252 spread=0.108 229s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 229s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 229s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 229s " chr4:178514600-178514725 log2=-0.098 spread=0.096 229s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 229s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 229s " chr5:1295312-1295381 log2=-0.690 spread=0.462 229s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 229s " chr5:25519857-25520034 log2=-0.015 spread=0.095 229s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 229s " chr5:38962338-38962525 log2=0.005 spread=0.019 229s " chr5:38966685-38966862 log2=0.006 spread=0.165 229s " chr5:38978620-38978763 log2=0.040 spread=0.030 229s " chr5:39074133-39074327 log2=-0.158 spread=0.139 229s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 229s " chr5:51030131-51030313 log2=-0.034 spread=0.192 229s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 229s " chr5:56168412-56168590 log2=0.479 spread=0.038 229s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 229s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 229s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 229s " chr5:86637023-86637168 log2=0.054 spread=0.111 229s " chr5:86642414-86642592 log2=0.254 spread=0.162 229s " chr5:86648912-86649096 log2=0.092 spread=0.062 229s " chr5:86670598-86670778 log2=0.222 spread=0.198 229s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 229s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 229s APC chr5:112101965-112102138 log2=0.104 spread=0.217 229s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 229s " chr5:170837567-170837631 log2=0.085 spread=0.349 229s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 229s " chr5:180046203-180046404 log2=-1.531 spread=0.722 229s " chr5:180076418-180076603 log2=-2.224 spread=1.416 229s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 229s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 229s " chr6:31939599-31940313 log2=-19.582 spread=0.181 229s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 229s " chr6:31946632-31946824 log2=-20.052 spread=0.088 229s " chr6:31947142-31947366 log2=-20.114 spread=0.066 229s " chr6:31948176-31948360 log2=-19.982 spread=0.149 229s " chr6:31948382-31948612 log2=-19.757 spread=0.165 229s " chr6:31948730-31949253 log2=-20.048 spread=0.014 229s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 229s " chr6:32164046-32164227 log2=-19.755 spread=0.189 229s " chr6:32164652-32164888 log2=-19.984 spread=0.154 229s " chr6:32165021-32165403 log2=-19.625 spread=0.196 229s " chr6:32166163-32166545 log2=-20.043 spread=0.072 229s " chr6:32166648-32166962 log2=-3.514 spread=5.742 229s " chr6:32168554-32168821 log2=-19.601 spread=0.197 229s " chr6:32168844-32169306 log2=-19.683 spread=0.166 229s " chr6:32169801-32170391 log2=-19.405 spread=0.205 229s " chr6:32171492-32171691 log2=-20.095 spread=0.101 229s " chr6:32171861-32172198 log2=-3.141 spread=7.288 229s " chr6:32178478-32178749 log2=-19.927 spread=0.164 229s " chr6:32180197-32180441 log2=-10.902 spread=9.532 229s " chr6:32180544-32180722 log2=-19.675 spread=0.186 229s " chr6:32180857-32181062 log2=-19.562 spread=0.227 229s " chr6:32181411-32181646 log2=-19.966 spread=0.171 229s " chr6:32181832-32182066 log2=-19.961 spread=0.172 229s " chr6:32182948-32183194 log2=-19.935 spread=0.168 229s " chr6:32184667-32185079 log2=-19.923 spread=0.165 229s " chr6:32185720-32185919 log2=-19.707 spread=0.197 229s " chr6:32187317-32187601 log2=-19.765 spread=0.173 229s " chr6:32187871-32188094 log2=-19.660 spread=0.188 229s " chr6:32188127-32188451 log2=-19.622 spread=0.169 229s " chr6:32188481-32188693 log2=-19.902 spread=0.132 229s " chr6:32188704-32189133 log2=-19.501 spread=0.193 229s " chr6:32190258-32190616 log2=-19.570 spread=0.209 229s " chr6:32190724-32190908 log2=-19.540 spread=0.232 229s " chr6:32191570-32191668 log2=-19.773 spread=0.178 229s " chr6:32191676-32191753 log2=-19.374 spread=0.201 229s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 229s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 229s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 229s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 229s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 229s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 229s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 229s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 229s " chr6:128316545-128316699 log2=-0.070 spread=0.050 229s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 229s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 229s " chr6:157099442-157099991 log2=-0.846 spread=0.504 229s " chr6:157100042-157100634 log2=-1.570 spread=0.825 229s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 229s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 229s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 229s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 229s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 229s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 229s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 229s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 229s " chr7:98491365-98491541 log2=0.209 spread=0.153 229s " chr7:98493314-98493496 log2=0.389 spread=0.207 229s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 229s " chr7:128829048-128829358 log2=-0.474 spread=0.315 229s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 229s " chr7:140484736-140484912 log2=0.081 spread=0.150 229s " chr7:140487956-140488430 log2=-0.089 spread=0.142 229s " chr7:140493336-140493442 log2=-0.340 spread=0.283 229s " chr7:140624315-140624540 log2=-0.497 spread=0.342 229s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 229s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 229s " chr8:30941153-30941335 log2=0.079 spread=0.294 229s " chr8:30942625-30942802 log2=0.044 spread=0.247 229s " chr8:30947918-30948092 log2=0.151 spread=0.124 229s " chr8:31000128-31000252 log2=-0.099 spread=0.098 229s " chr8:31001006-31001182 log2=-0.002 spread=0.062 229s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 229s " chr8:37698557-37699898 log2=-0.612 spread=0.029 229s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 229s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 229s " chr8:48845528-48845758 log2=0.056 spread=0.196 229s " chr8:48866846-48867043 log2=-0.067 spread=0.097 229s " chr8:48868369-48868526 log2=-0.239 spread=0.174 229s " chr8:48872485-48872722 log2=-0.636 spread=0.464 229s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 229s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 229s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 229s " chr9:2101491-2101640 log2=0.244 spread=0.104 229s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 229s " chr9:5067014-5067883 log2=0.146 spread=0.089 229s " chr9:5068184-5070306 log2=0.133 spread=0.092 229s " chr9:5076944-5077152 log2=0.046 spread=0.137 229s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 229s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 229s " chr9:21986759-21986899 log2=0.058 spread=0.175 229s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 229s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 229s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 229s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 229s " chr9:87425375-87425452 log2=0.494 spread=0.066 229s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 229s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 229s " chr9:139250747-139251032 log2=-0.223 spread=0.273 229s " chr9:139252418-139252703 log2=-0.512 spread=0.264 229s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 229s " chr9:139417262-139417677 log2=-0.173 spread=0.191 229s " chr9:139440110-139440287 log2=-1.257 spread=0.500 229s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 229s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 229s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 229s " chr10:43600360-43600677 log2=-0.341 spread=0.222 229s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 229s " chr10:89685254-89685374 log2=0.244 spread=0.259 229s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 229s " chr10:93579008-93579121 log2=0.166 spread=0.220 229s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 229s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 229s " chr10:112679716-112679934 log2=-0.008 spread=0.028 229s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 229s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 229s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 229s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 229s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 229s " chr11:94170270-94170454 log2=0.095 spread=0.285 229s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 229s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 229s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 229s " chr11:108164020-108164234 log2=-0.056 spread=0.040 229s " chr11:108217986-108218135 log2=0.359 spread=0.277 229s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 229s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 229s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 229s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 229s " chr12:25391004-25391186 log2=0.368 spread=0.128 229s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 229s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 229s " chr12:51206782-51207287 log2=-0.012 spread=0.101 229s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 229s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 229s " chr13:26970356-26970536 log2=0.137 spread=0.121 229s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 229s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 229s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 229s " chr13:32903506-32903689 log2=0.019 spread=0.232 229s " chr13:32918645-32918823 log2=0.158 spread=0.114 229s " chr13:32920899-32921077 log2=0.014 spread=0.247 229s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 229s " chr13:48919164-48919369 log2=0.025 spread=0.094 229s " chr13:48921877-48922044 log2=0.106 spread=0.147 229s " chr13:48923026-48923204 log2=0.360 spread=0.016 229s " chr13:48938965-48939147 log2=0.084 spread=0.356 229s " chr13:48941578-48941767 log2=0.238 spread=0.212 229s " chr13:48947486-48947665 log2=0.025 spread=0.126 229s " chr13:48954166-48954251 log2=0.061 spread=0.273 229s " chr13:49037815-49038005 log2=0.063 spread=0.062 229s " chr13:49047410-49047589 log2=0.053 spread=0.170 229s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 229s " chr13:85527771-85527948 log2=0.007 spread=0.222 229s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 229s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 229s " chr13:110438332-110438432 log2=-3.643 spread=2.325 229s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 229s " chr14:20291466-20291612 log2=0.697 spread=0.248 229s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 229s " chr14:36989195-36989373 log2=0.023 spread=0.162 229s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 229s " chr14:50619741-50619923 log2=0.003 spread=0.272 229s " chr14:50697856-50698044 log2=0.277 spread=0.334 229s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 229s " chr14:71275790-71275923 log2=-2.815 spread=1.938 229s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 229s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 229s " chr15:38544477-38545455 log2=-0.348 spread=0.179 229s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 229s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 229s " chr15:41803968-41804185 log2=-2.202 spread=0.188 229s " chr15:41804261-41804494 log2=-0.402 spread=0.392 229s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 229s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 229s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 229s " chr16:2611404-2611585 log2=-5.171 spread=1.963 229s " chr16:2611721-2611943 log2=-11.810 spread=9.172 229s " chr16:2615504-2615725 log2=-20.113 spread=0.007 229s " chr16:2616307-2616486 log2=-20.054 spread=0.072 229s " chr16:2631267-2631414 log2=-20.009 spread=0.061 229s " chr16:2631583-2631734 log2=-20.089 spread=0.090 229s " chr16:2633363-2633616 log2=-20.101 spread=0.089 229s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 229s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 229s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 229s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 229s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 229s " chr16:50826460-50826650 log2=0.239 spread=0.204 229s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 229s " chr16:60005694-60005857 log2=-0.366 spread=0.298 229s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 229s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 229s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 229s " chr17:12011053-12011253 log2=0.028 spread=0.232 229s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 229s " chr17:29496854-29497046 log2=0.226 spread=0.193 229s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 229s " chr17:30519172-30519355 log2=0.163 spread=0.289 229s " chr17:30525911-30526093 log2=-0.157 spread=0.046 229s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 229s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 229s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 229s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 229s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 229s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 229s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 229s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 229s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 229s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 229s " chr19:2210351-2210545 log2=-0.860 spread=0.261 229s " chr19:2226130-2227152 log2=-0.113 spread=0.120 229s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 229s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 229s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 229s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 229s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 229s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 229s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 229s " chr19:15311544-15311749 log2=-1.887 spread=1.202 229s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 229s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 229s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 229s " chr19:33792774-33793010 log2=-1.781 spread=0.127 229s " chr19:33793014-33793356 log2=-0.541 spread=0.385 229s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 229s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 229s " chr19:45873698-45873881 log2=-0.522 spread=0.327 229s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 229s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 229s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 229s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 229s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 229s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 229s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 229s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 229s " chr21:36265140-36265318 log2=0.042 spread=0.039 229s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 229s " chr22:29115325-29115465 log2=0.055 spread=0.390 229s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 229s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 229s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 229s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 229s " chrX:1317372-1317594 log2=-21.121 spread=0.049 229s " chrX:1321225-1321435 log2=-20.851 spread=0.196 229s " chrX:1325274-1325530 log2=-21.121 spread=0.011 229s " chrX:1327651-1327830 log2=-21.000 spread=0.029 229s " chrX:1331391-1331576 log2=-21.018 spread=0.052 229s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 229s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 229s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 229s " chrX:123185143-123185290 log2=-1.018 spread=0.062 229s " chrX:123202378-123202544 log2=-0.959 spread=0.103 229s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 229s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 229s " chrY:9008607-9008759 log2=-1.012 spread=0.097 229s " chrY:13131970-13132039 log2=-1.004 spread=0.074 229s " chrY:19506485-19506650 log2=-1.018 spread=0.034 229s " chrY:21033918-21034071 log2=-1.013 spread=0.057 229s " chrY:28463435-28463622 log2=-0.952 spread=0.039 229s " chrY:28514033-28514208 log2=-0.992 spread=0.026 229s Antitargets: 108 (0.8597%) bins failed filters 229s Wrote build/reference-picard.cnn with 19209 regions 230s 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 232s Processing target: p2-5_5 232s Keeping 6308 of 6646 bins 232s Correcting for GC bias... 232s Correcting for density bias... 232s Processing antitarget: p2-5_5 232s Keeping 12455 of 12563 bins 232s Correcting for GC bias... 232s WARNING: Skipping correction for RepeatMasker bias 232s Targets are 1.18 x more variable than antitargets 232s Wrote build/p2-5_5.cnr with 18763 regions 233s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 236s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 236s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 236s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 237s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 237s 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 239s Processing target: p2-9_2 239s Keeping 6308 of 6646 bins 239s Correcting for GC bias... 239s Correcting for density bias... 239s Processing antitarget: p2-9_2 239s Keeping 12455 of 12563 bins 239s Correcting for GC bias... 239s WARNING: Skipping correction for RepeatMasker bias 239s Targets are 1.72 x more variable than antitargets 240s Wrote build/p2-9_2.cnr with 18763 regions 240s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 241s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 242s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 242s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 244s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 244s 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 246s Processing target: p2-20_1 246s Keeping 6308 of 6646 bins 246s Correcting for GC bias... 246s Correcting for density bias... 246s Processing antitarget: p2-20_1 246s Keeping 12455 of 12563 bins 246s Correcting for GC bias... 246s WARNING: Skipping correction for RepeatMasker bias 246s Targets are 1.12 x more variable than antitargets 247s Wrote build/p2-20_1.cnr with 18763 regions 247s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 249s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 249s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 249s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 251s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 251s 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 253s Processing target: p2-20_2 253s Keeping 6308 of 6646 bins 253s Correcting for GC bias... 253s Correcting for density bias... 253s Processing antitarget: p2-20_2 254s Keeping 12455 of 12563 bins 254s Correcting for GC bias... 254s WARNING: Skipping correction for RepeatMasker bias 254s Targets are 1.10 x more variable than antitargets 254s Wrote build/p2-20_2.cnr with 18763 regions 255s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 256s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 256s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 257s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 258s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 259s 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 260s Processing target: p2-20_3 261s Keeping 6308 of 6646 bins 261s Correcting for GC bias... 261s Correcting for density bias... 261s Processing antitarget: p2-20_3 261s Keeping 12455 of 12563 bins 261s Correcting for GC bias... 261s WARNING: Skipping correction for RepeatMasker bias 261s Antitargets are 1.09 x more variable than targets 261s Wrote build/p2-20_3.cnr with 18763 regions 262s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 263s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 263s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 264s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 265s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 266s 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 267s Processing target: p2-20_4 267s Keeping 6308 of 6646 bins 268s Correcting for GC bias... 268s Correcting for density bias... 268s Processing antitarget: p2-20_4 268s Keeping 12455 of 12563 bins 268s Correcting for GC bias... 268s WARNING: Skipping correction for RepeatMasker bias 268s Targets are 1.43 x more variable than antitargets 268s Wrote build/p2-20_4.cnr with 18763 regions 269s 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 270s Processing target: p2-20_5 270s Keeping 6308 of 6646 bins 270s Correcting for GC bias... 270s Correcting for density bias... 270s Processing antitarget: p2-20_5 271s Keeping 12455 of 12563 bins 271s Correcting for GC bias... 271s WARNING: Skipping correction for RepeatMasker bias 271s Targets are 2.50 x more variable than antitargets 271s Wrote build/p2-20_5.cnr with 18763 regions 271s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 273s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 280s Dropped 8 / 49 bins on chromosome chrY 280s Wrote build/p2-5_5.cns with 71 regions 281s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 282s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 284s Dropped 1 / 949 bins on chromosome chr6 289s Dropped 27 / 49 bins on chromosome chrY 290s Wrote build/p2-9_2.cns with 103 regions 290s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 292s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 299s Dropped 6 / 49 bins on chromosome chrY 299s Wrote build/p2-20_1.cns with 121 regions 300s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 302s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 309s Dropped 7 / 49 bins on chromosome chrY 309s Wrote build/p2-20_2.cns with 117 regions 310s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 311s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 319s Dropped 11 / 49 bins on chromosome chrY 319s Wrote build/p2-20_3.cns with 64 regions 319s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 321s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 329s Dropped 8 / 49 bins on chromosome chrY 329s Wrote build/p2-20_4.cns with 143 regions 329s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 331s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 338s Smoothing overshot at 1 / 123 indices: (-0.30060035404086677, 0.32508880185194816) vs. original (-0.363302, 0.311218) 338s Dropped 6 / 49 bins on chromosome chrY 339s Wrote build/p2-20_5.cns with 120 regions 339s 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 342s Wrote p2-5_5-scatter.pdf 342s 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 344s Smoothing overshot at 3 / 97 indices: (-19.900105868621715, -3.3099069223720554) vs. original (-19.294, -0.16431) 345s Wrote p2-9_2-scatter.pdf 346s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 347s Showing 1480 probes and 0 selected genes in region chr1 348s Wrote p2-9_2-chr1-scatter.pdf 348s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 350s Showing 201 probes and 0 selected genes in region chr21 350s Wrote p2-9_2-chr21-scatter.pdf 350s 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 352s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 353s Wrote p2-9_2-chr9p-scatter.pdf 353s 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 355s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 355s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 355s 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 357s Detected file format: bed 357s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 357s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 357s 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 357s /usr/bin/pdfunite 357s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 359s Treating sample p2-5_5 as female 368s Wrote p2-5_5-diagram.pdf 369s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 370s Treating sample p2-9_2 as female 379s Wrote p2-9_2-diagram.pdf 380s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 381s Treating sample p2-20_1 as female 390s Wrote p2-20_1-diagram.pdf 390s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 392s Treating sample p2-20_2 as female 401s Wrote p2-20_2-diagram.pdf 401s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 402s Treating sample p2-5_5 as female 402s Wrote p2-5_5-cbs-diagram.pdf 403s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 404s Treating sample p2-9_2 as female 405s Wrote p2-9_2-cbs-diagram.pdf 405s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 407s Treating sample p2-20_1 as female 407s Wrote p2-20_1-cbs-diagram.pdf 407s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 409s Treating sample p2-20_2 as female 409s Wrote p2-20_2-cbs-diagram.pdf 409s 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 411s Treating sample p2-5_5 as female 416s Wrote p2-5_5-both-diagram.pdf 417s 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 418s Treating sample p2-9_2 as female 424s Wrote p2-9_2-both-diagram.pdf 424s 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 426s Treating sample p2-20_1 as female 431s Wrote p2-20_1-both-diagram.pdf 432s 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 433s Treating sample p2-20_2 as female 439s Wrote p2-20_2-both-diagram.pdf 440s 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 440s /usr/bin/pdfunite 440s 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 441s Treating sample p2-5_5 as female 441s Treating sample p2-9_2 as female 441s Treating sample p2-20_1 as female 441s Treating sample p2-20_2 as female 441s Treating sample p2-20_3 as female 441s Treating sample p2-20_4 as female 441s Treating sample p2-20_5 as female 443s Wrote heatmap-picard.pdf 443s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 445s Found 14 gene breakpoints 445s Wrote p2-9_2-breaks.txt 445s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 447s Treating sample p2-9_2 as female 449s Found 323 gene-level gains and losses 449s Wrote p2-9_2-genemetrics.txt 449s 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 451s Wrote gender-picard.txt 451s 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 456s Wrote p2-all.cdt 456s 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 461s Wrote p2-all-jtv.txt 461s 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 463s Wrote p2-all.seg 464s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 466s Wrote p2-9_2.nexus 466s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 468s Selected test sample NA12882 and control sample NA12878 468s Loaded 3654 records; skipped: 514 somatic, 394 depth 468s Kept 2631 heterozygous of 3654 VCF records 470s Placed 705 variants into 18763 bins 470s Wrote p2-9_2.nexus-ogt 471s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 472s Treating sample p2-5_5 as female 472s Rescaling sample with purity 0.65, ploidy 2 472s Wrote build/p2-5_5.call.cns with 71 regions 473s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 474s Treating sample p2-9_2 as female 474s Rescaling sample with purity 0.65, ploidy 2 474s Wrote build/p2-9_2.call.cns with 103 regions 475s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 476s Treating sample p2-20_1 as female 476s Rescaling sample with purity 0.65, ploidy 2 476s Wrote build/p2-20_1.call.cns with 121 regions 477s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 478s Treating sample p2-20_2 as female 478s Rescaling sample with purity 0.65, ploidy 2 478s Wrote build/p2-20_2.call.cns with 117 regions 479s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 480s Treating sample p2-20_3 as female 480s Rescaling sample with purity 0.65, ploidy 2 480s Wrote build/p2-20_3.call.cns with 64 regions 481s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 482s Treating sample p2-20_4 as female 482s Rescaling sample with purity 0.65, ploidy 2 482s Wrote build/p2-20_4.call.cns with 143 regions 483s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 485s Treating sample p2-20_5 as female 485s Rescaling sample with purity 0.65, ploidy 2 485s Wrote build/p2-20_5.call.cns with 120 regions 485s 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 487s Treating sample p2-5_5.call as female 487s Treating sample p2-9_2.call as female 487s Treating sample p2-20_1.call as female 487s Treating sample p2-20_2.call as female 487s Treating sample p2-20_3.call as female 487s Treating sample p2-20_4.call as female 487s Treating sample p2-20_5.call as female 487s Wrote p2-all.bed 487s 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 489s Treating sample p2-9_2.call as female 489s Wrote p2-9_2.vcf 490s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 491s /usr/lib/python3/dist-packages/cnvlib/export.py:489: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 491s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 491s Wrote p2-9_2.theta2.input 493s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 493s --mean --median --mode --t-test \ 493s --stdev --mad --mse --iqr --bivar \ 493s --ci --pi --sem --smooth-bootstrap 495s Wrote p2-9_2-segmetrics.cns with 103 regions 495s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 495s --ci -b 50 -a 0.5 497s Wrote p2-5_5-segmetrics.cns with 71 regions 497s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 499s Wrote p2-5_5-metrics.tsv 500s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 501s Wrote p2-9_2-metrics.tsv 502s 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 504s Wrote p2-20-metrics.tsv 505s PASS 505s autopkgtest [09:02:46]: test run-unit-test: -----------------------] 506s run-unit-test PASS 506s autopkgtest [09:02:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 506s autopkgtest [09:02:47]: test pybuild-autopkgtest: preparing testbed 511s Reading package lists... 511s Building dependency tree... 511s Reading state information... 511s Starting pkgProblemResolver with broken count: 0 511s Starting 2 pkgProblemResolver with broken count: 0 511s Done 512s The following additional packages will be installed: 512s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 512s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 512s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 512s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 512s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 512s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 512s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 512s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev 512s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 512s pybuild-plugin-pyproject python3-all python3-build python3-iniconfig 512s python3-installer python3-pluggy python3-pyproject-hooks python3-pytest 512s python3-toml python3-wheel python3.13 python3.13-minimal 512s Suggested packages: 512s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 512s cpp-14-doc dh-make flit gcc-14-doc gcc-multilib manpages-dev flex bison gdb 512s gcc-doc gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 512s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 512s libmail-box-perl python3-pip python3-venv python-build-doc 512s python-installer-doc python3.13-venv python3.13-doc binfmt-support 512s Recommended packages: 512s libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 512s The following NEW packages will be installed: 512s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 512s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 512s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 512s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 512s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 512s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 512s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 512s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libstdc++-14-dev 512s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 512s pybuild-plugin-pyproject python3-all python3-build python3-iniconfig 512s python3-installer python3-pluggy python3-pyproject-hooks python3-pytest 512s python3-toml python3-wheel python3.13 python3.13-minimal 512s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 512s Need to get 70.5 MB/70.5 MB of archives. 512s After this operation, 246 MB of additional disk space will be used. 512s Get:1 /tmp/autopkgtest.DAZmaz/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [864 B] 512s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 513s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 513s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 513s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 513s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 513s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 513s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 513s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 513s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 513s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 513s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 513s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 513s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 513s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 513s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 513s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 513s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 513s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 513s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 513s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 514s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 514s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 514s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 514s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 514s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 514s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 514s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 514s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 514s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 514s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 514s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 514s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 514s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 515s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 515s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 515s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 515s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 515s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 515s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 515s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 515s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 515s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 515s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 515s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 515s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 515s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 515s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 515s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-toml all 0.10.2-1 [16.5 kB] 515s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-wheel all 0.44.0-1 [54.2 kB] 515s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-build all 1.2.2-1 [31.0 kB] 515s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 515s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 515s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 515s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 515s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 515s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 515s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 515s Fetched 70.5 MB in 3s (27.0 MB/s) 515s Selecting previously unselected package libpython3.13-minimal:arm64. 515s (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 ... 97150 files and directories currently installed.) 515s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 515s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 515s Selecting previously unselected package python3.13-minimal. 516s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 516s Unpacking python3.13-minimal (3.13.0-2) ... 516s Selecting previously unselected package m4. 516s Preparing to unpack .../02-m4_1.4.19-4build1_arm64.deb ... 516s Unpacking m4 (1.4.19-4build1) ... 516s Selecting previously unselected package autoconf. 516s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 516s Unpacking autoconf (2.72-3) ... 516s Selecting previously unselected package autotools-dev. 516s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 516s Unpacking autotools-dev (20220109.1) ... 516s Selecting previously unselected package automake. 516s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 516s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 516s Selecting previously unselected package autopoint. 516s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 516s Unpacking autopoint (0.22.5-2) ... 516s Selecting previously unselected package libisl23:arm64. 516s Preparing to unpack .../07-libisl23_0.27-1_arm64.deb ... 516s Unpacking libisl23:arm64 (0.27-1) ... 516s Selecting previously unselected package libmpc3:arm64. 516s Preparing to unpack .../08-libmpc3_1.3.1-1build2_arm64.deb ... 516s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 516s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 516s Preparing to unpack .../09-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 516s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 516s Selecting previously unselected package cpp-14. 516s Preparing to unpack .../10-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 516s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 516s Selecting previously unselected package cpp-aarch64-linux-gnu. 516s Preparing to unpack .../11-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 516s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 516s Selecting previously unselected package cpp. 517s Preparing to unpack .../12-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 517s Unpacking cpp (4:14.1.0-2ubuntu1) ... 517s Selecting previously unselected package libcc1-0:arm64. 517s Preparing to unpack .../13-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libitm1:arm64. 517s Preparing to unpack .../14-libitm1_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libasan8:arm64. 517s Preparing to unpack .../15-libasan8_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package liblsan0:arm64. 517s Preparing to unpack .../16-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libtsan2:arm64. 517s Preparing to unpack .../17-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libubsan1:arm64. 517s Preparing to unpack .../18-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libhwasan0:arm64. 517s Preparing to unpack .../19-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package libgcc-14-dev:arm64. 517s Preparing to unpack .../20-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 517s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 517s Preparing to unpack .../21-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 517s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 519s Selecting previously unselected package gcc-14. 519s Preparing to unpack .../22-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 519s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 519s Selecting previously unselected package gcc-aarch64-linux-gnu. 519s Preparing to unpack .../23-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 519s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 519s Selecting previously unselected package gcc. 519s Preparing to unpack .../24-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 519s Unpacking gcc (4:14.1.0-2ubuntu1) ... 519s Selecting previously unselected package libstdc++-14-dev:arm64. 519s Preparing to unpack .../25-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 519s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 519s Selecting previously unselected package g++-14-aarch64-linux-gnu. 519s Preparing to unpack .../26-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 519s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 519s Selecting previously unselected package g++-14. 519s Preparing to unpack .../27-g++-14_14.2.0-8ubuntu1_arm64.deb ... 519s Unpacking g++-14 (14.2.0-8ubuntu1) ... 519s Selecting previously unselected package g++-aarch64-linux-gnu. 519s Preparing to unpack .../28-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 519s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 519s Selecting previously unselected package g++. 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(4:14.1.0-2ubuntu1) ... 526s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 526s Setting up build-essential (12.10ubuntu1) ... 526s Setting up debhelper (13.20ubuntu1) ... 526s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 526s Setting up autopkgtest-satdep (0) ... 526s Processing triggers for systemd (256.5-2ubuntu4) ... 526s Processing triggers for man-db (2.12.1-3) ... 527s Processing triggers for install-info (7.1.1-1) ... 527s Processing triggers for libc-bin (2.40-1ubuntu3) ... 530s (Reading database ... 100427 files and directories currently installed.) 530s Removing autopkgtest-satdep (0) ... 531s autopkgtest [09:03:12]: test pybuild-autopkgtest: pybuild-autopkgtest 531s autopkgtest [09:03:12]: test pybuild-autopkgtest: [----------------------- 531s pybuild-autopkgtest 531s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.DAZmaz/build.NOT/src/data /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/data; 531s I: pybuild base:311: cd /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build; python3.13 -m pytest test 532s ============================= test session starts ============================== 532s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 532s rootdir: /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build 532s configfile: pyproject.toml 532s plugins: typeguard-4.4.1 532s collected 0 items / 5 errors 532s 532s ==================================== ERRORS ==================================== 532s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 532s ImportError while importing test module '/tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/test/test_cnvlib.py'. 532s Hint: make sure your test modules/packages have valid Python names. 532s Traceback: 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 532s from . import multiarray 532s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 532s from . import overrides 532s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 532s from numpy.core._multiarray_umath import ( 532s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 532s 532s During handling of the above exception, another exception occurred: 532s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 532s from numpy.__config__ import show as show_config 532s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 532s from numpy.core._multiarray_umath import ( 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 532s raise ImportError(msg) 532s E ImportError: 532s E 532s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 532s E 532s E Importing the numpy C-extensions failed. This error can happen for 532s E many reasons, often due to issues with your setup or how NumPy was 532s E installed. 532s E 532s E We have compiled some common reasons and troubleshooting tips at: 532s E 532s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 532s E 532s E Please note and check the following: 532s E 532s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 532s E * The NumPy version is: "1.26.4" 532s E 532s E and make sure that they are the versions you expect. 532s E Please carefully study the documentation linked above for further help. 532s E 532s E Original error was: No module named 'numpy.core._multiarray_umath' 532s 532s The above exception was the direct cause of the following exception: 532s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 532s return _bootstrap._gcd_import(name[level:], package, level) 532s test/test_cnvlib.py:15: in 532s import numpy as np 532s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 532s raise ImportError(msg) from e 532s E ImportError: Error importing numpy: you should not try to import numpy from 532s E its source directory; please exit the numpy source tree, and relaunch 532s E your python interpreter from there. 532s ____________________ ERROR collecting test/test_commands.py ____________________ 532s ImportError while importing test module '/tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/test/test_commands.py'. 532s Hint: make sure your test modules/packages have valid Python names. 532s Traceback: 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 532s from . import multiarray 532s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 532s from . import overrides 532s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 532s from numpy.core._multiarray_umath import ( 532s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 532s 532s During handling of the above exception, another exception occurred: 532s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 532s from numpy.__config__ import show as show_config 532s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 532s from numpy.core._multiarray_umath import ( 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 532s raise ImportError(msg) 532s E ImportError: 532s E 532s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 532s E 532s E Importing the numpy C-extensions failed. This error can happen for 532s E many reasons, often due to issues with your setup or how NumPy was 532s E installed. 532s E 532s E We have compiled some common reasons and troubleshooting tips at: 532s E 532s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 532s E 532s E Please note and check the following: 532s E 532s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 532s E * The NumPy version is: "1.26.4" 532s E 532s E and make sure that they are the versions you expect. 532s E Please carefully study the documentation linked above for further help. 532s E 532s E Original error was: No module named 'numpy.core._multiarray_umath' 532s 532s The above exception was the direct cause of the following exception: 532s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 532s return _bootstrap._gcd_import(name[level:], package, level) 532s test/test_commands.py:16: in 532s import numpy as np 532s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 532s raise ImportError(msg) from e 532s E ImportError: Error importing numpy: you should not try to import numpy from 532s E its source directory; please exit the numpy source tree, and relaunch 532s E your python interpreter from there. 532s _____________________ ERROR collecting test/test_genome.py _____________________ 532s ImportError while importing test module '/tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/test/test_genome.py'. 532s Hint: make sure your test modules/packages have valid Python names. 532s Traceback: 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 532s from . import multiarray 532s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 532s from . import overrides 532s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 532s from numpy.core._multiarray_umath import ( 532s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 532s 532s During handling of the above exception, another exception occurred: 532s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 532s from numpy.__config__ import show as show_config 532s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 532s from numpy.core._multiarray_umath import ( 532s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 532s raise ImportError(msg) 532s E ImportError: 532s E 532s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 532s E 532s E Importing the numpy C-extensions failed. This error can happen for 532s E many reasons, often due to issues with your setup or how NumPy was 532s E installed. 532s E 532s E We have compiled some common reasons and troubleshooting tips at: 532s E 532s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 532s E 532s E Please note and check the following: 532s E 532s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 532s E * The NumPy version is: "1.26.4" 532s E 532s E and make sure that they are the versions you expect. 532s E Please carefully study the documentation linked above for further help. 532s E 532s E Original error was: No module named 'numpy.core._multiarray_umath' 532s 532s The above exception was the direct cause of the following exception: 532s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 532s return _bootstrap._gcd_import(name[level:], package, level) 532s test/test_genome.py:12: in 532s import numpy as np 532s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 532s raise ImportError(msg) from e 532s E ImportError: Error importing numpy: you should not try to import numpy from 532s E its source directory; please exit the numpy source tree, and relaunch 532s E your python interpreter from there. 532s _______________________ ERROR collecting test/test_io.py _______________________ 532s ImportError while importing test module '/tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/test/test_io.py'. 532s Hint: make sure your test modules/packages have valid Python names. 532s Traceback: 532s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 532s return _bootstrap._gcd_import(name[level:], package, level) 532s test/test_io.py:11: in 532s from skgenome import tabio 532s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 532s from . import tabio 532s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 532s import pandas as pd 532s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 532s raise ImportError( 532s E ImportError: Unable to import required dependencies: 532s E numpy: Error importing numpy: you should not try to import numpy from 532s E its source directory; please exit the numpy source tree, and relaunch 532s E your python interpreter from there. 532s _______________________ ERROR collecting test/test_r.py ________________________ 532s ImportError while importing test module '/tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/test/test_r.py'. 532s Hint: make sure your test modules/packages have valid Python names. 532s Traceback: 532s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 532s return _bootstrap._gcd_import(name[level:], package, level) 532s test/test_r.py:14: in 532s import cnvlib 532s /usr/lib/python3/dist-packages/cnvlib/__init__.py:1: in 532s from skgenome.tabio import write 532s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 532s from . import tabio 532s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 532s import pandas as pd 532s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 532s raise ImportError( 532s E ImportError: Unable to import required dependencies: 532s E numpy: Error importing numpy: you should not try to import numpy from 532s E its source directory; please exit the numpy source tree, and relaunch 532s E your python interpreter from there. 532s =========================== short test summary info ============================ 532s ERROR test/test_cnvlib.py 532s ERROR test/test_commands.py 532s ERROR test/test_genome.py 532s ERROR test/test_io.py 532s ERROR test/test_r.py 532s !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! 532s ============================== 5 errors in 0.33s =============================== 532s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build; python3.13 -m pytest test 532s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.DAZmaz/build.NOT/src/data /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build/data; 532s I: pybuild base:311: cd /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build; python3.12 -m pytest test 535s ============================= test session starts ============================== 535s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 535s rootdir: /tmp/autopkgtest.DAZmaz/autopkgtest_tmp/build 535s configfile: pyproject.toml 535s plugins: typeguard-4.4.1 535s collected 64 items 535s 541s test/test_cnvlib.py ......... [ 14%] 562s test/test_commands.py ......................... [ 53%] 568s test/test_genome.py ................... [ 82%] 569s test/test_io.py .......... [ 98%] 580s test/test_r.py . [100%] 580s 580s =============================== warnings summary =============================== 580s test/test_commands.py::CommandTests::test_antitarget 580s test/test_commands.py::CommandTests::test_target 580s test/test_genome.py::GaryTests::test_ranges_resize 580s test/test_io.py::IOTests::test_empty 580s test/test_io.py::IOTests::test_read_auto 580s test/test_io.py::IOTests::test_read_auto 580s test/test_io.py::IOTests::test_read_ilist 580s /usr/lib/python3/dist-packages/skgenome/tabio/picard.py:27: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. 580s The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. 580s 580s For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. 580s 580s 580s dframe["gene"].fillna("-", inplace=True) 580s 580s test/test_commands.py: 11 warnings 580s test/test_genome.py: 6 warnings 580s /usr/lib/python3/dist-packages/skgenome/merge.py:149: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. 580s .apply(_merge_overlapping, bp, cmb) 580s 580s test/test_commands.py::CommandTests::test_batch 580s /usr/lib/python3/dist-packages/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[0. 0. 0. 0. 0. 0. 580s 0. 0. 0. 0. 0. 0. 580s 0. 0. 0. 0. 0. 0. 580s 0. 0. 0. 1.20240481 0.31062124 0.89178357 580s 0. 0. 0. 1.20240481 0.4 0.2004008 580s 0. 0.4008016 0.4 0.4008016 0. 0. 580s 0. 0.4008016 0. 1.20240481 0. 0. 580s 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 580s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 580s 580s test/test_commands.py::CommandTests::test_batch 580s test/test_commands.py::CommandTests::test_batch 580s /usr/lib/python3/dist-packages/cnvlib/reference.py:187: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. 580s ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) 580s 580s test/test_commands.py::CommandTests::test_batch 580s test/test_commands.py::CommandTests::test_batch 580s /usr/lib/python3/dist-packages/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[ 3. 3. 3. 3.09090909 4. 4. 580s 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 580s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 580s 580s test/test_commands.py: 19 warnings 580s /usr/lib/python3/dist-packages/cnvlib/segfilters.py:72: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. 580s .apply(squash_region) 580s 580s test/test_commands.py: 10 warnings 580s /usr/lib/python3/dist-packages/cnvlib/segfilters.py:59: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 580s chrom_col = cnarr["chromosome"].replace( 580s 580s test/test_commands.py::CommandTests::test_coverage 580s test/test_commands.py::CommandTests::test_coverage 580s test/test_commands.py::CommandTests::test_coverage 580s test/test_commands.py::CommandTests::test_coverage 580s /usr/lib/python3/dist-packages/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[82.5 3.02325581 4. 3.88888889]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 580s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 580s 580s test/test_commands.py::CommandTests::test_export_theta 580s test/test_commands.py::CommandTests::test_export_theta 580s /usr/lib/python3/dist-packages/cnvlib/export.py:489: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 580s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 580s 580s test/test_commands.py: 8 warnings 580s test/test_genome.py: 21 warnings 580s /usr/lib/python3/dist-packages/skgenome/gary.py:90: FutureWarning: Passing a DataFrame to DataFrame.from_records is deprecated. Use set_index and/or drop to modify the DataFrame instead. 580s table = pd.DataFrame.from_records(rows, columns=columns) 580s 580s test/test_commands.py::CommandTests::test_target 580s test/test_commands.py::CommandTests::test_target 580s test/test_commands.py::CommandTests::test_target 580s test/test_commands.py::CommandTests::test_target 580s test/test_commands.py::CommandTests::test_target 580s test/test_commands.py::CommandTests::test_target 580s test/test_genome.py::GaryTests::test_total_range_size 580s test/test_genome.py::GaryTests::test_total_range_size 580s /usr/lib/python3/dist-packages/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version. 580s return sep.join(pd.unique(elems)) 580s 580s test/test_genome.py::GaryTests::test_ranges_resize 580s /usr/lib/python3/dist-packages/skgenome/gary.py:669: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 580s limits["upper"] = self.chromosome.replace(chrom_sizes) 580s 580s test/test_genome.py::IntervalTests::test_flatten 580s test/test_genome.py::IntervalTests::test_flatten 580s /usr/lib/python3/dist-packages/skgenome/merge.py:29: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. 580s .apply(_flatten_overlapping, cmb, split_columns) 580s 580s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 580s ====================== 64 passed, 104 warnings in 47.51s ======================= 581s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 581s make: *** [/tmp/fV5jd2SsCN/run:4: pybuild-autopkgtest] Error 25 581s pybuild-autopkgtest: error: /tmp/fV5jd2SsCN/run pybuild-autopkgtest returned exit code 2 581s autopkgtest [09:04:02]: test pybuild-autopkgtest: -----------------------] 582s autopkgtest [09:04:03]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 582s pybuild-autopkgtest FAIL non-zero exit status 25 582s autopkgtest [09:04:03]: @@@@@@@@@@@@@@@@@@@@ summary 582s run-unit-test PASS 582s pybuild-autopkgtest FAIL non-zero exit status 25 602s nova [W] Skipping flock in bos03-arm64 602s Creating nova instance adt-plucky-arm64-cnvkit-20241113-085421-juju-7f2275-prod-proposed-migration-environment-15-6d1967ba-0d00-475c-b084-f692800b121d from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...