0s autopkgtest [08:11:57]: starting date and time: 2024-11-13 08:11:57+0000 0s autopkgtest [08:11:57]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:11:57]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v6w1jr7h/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-24.secgroup --name adt-plucky-amd64-cnvkit-20241113-081157-juju-7f2275-prod-proposed-migration-environment-20-4aadc13f-6f8c-4de1-b7cf-b80425658c98 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 65s autopkgtest [08:13:02]: testbed dpkg architecture: amd64 65s autopkgtest [08:13:02]: testbed apt version: 2.9.8 65s autopkgtest [08:13:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 67s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [848 kB] 68s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 68s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 68s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 68s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 68s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 68s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 68s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 68s Fetched 2171 kB in 2s (1205 kB/s) 68s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade... 71s The following NEW packages will be installed: 71s python3.13-gdbm 71s The following packages will be upgraded: 71s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 71s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 253 kB of archives. 71s After this operation, 147 kB of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 71s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 71s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 71s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 71s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 71s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 72s Fetched 253 kB in 0s (611 kB/s) 72s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 72s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 72s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 72s Setting up python3-minimal (3.12.7-1) ... 72s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75541 files and directories currently installed.) 72s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 72s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 72s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 72s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 72s Selecting previously unselected package python3.13-gdbm. 72s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 72s Unpacking python3.13-gdbm (3.13.0-2) ... 72s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 72s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 72s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 72s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 72s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 72s Setting up python3.13-gdbm (3.13.0-2) ... 72s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 72s Setting up python3 (3.12.7-1) ... 72s Setting up python3-gdbm:amd64 (3.12.7-1) ... 72s Processing triggers for man-db (2.12.1-3) ... 73s Processing triggers for libc-bin (2.40-1ubuntu3) ... 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 74s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 75s Reading package lists... 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s autopkgtest [08:13:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 79s autopkgtest [08:13:16]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 81s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (dsc) [2449 B] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (tar) [23.7 MB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (diff) [17.7 kB] 81s gpgv: Signature made Mon Apr 8 08:42:55 2024 UTC 81s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 81s gpgv: Can't check signature: No public key 81s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found 82s autopkgtest [08:13:19]: testing package cnvkit version 0.9.10-2 82s autopkgtest [08:13:19]: build not needed 85s autopkgtest [08:13:22]: test run-unit-test: preparing testbed 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Starting pkgProblemResolver with broken count: 0 88s Starting 2 pkgProblemResolver with broken count: 0 88s Done 88s The following additional packages will be installed: 88s blt cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 88s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 libdeflate0 88s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 88s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 88s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 88s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 88s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 88s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 88s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 88s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 88s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 88s python3-cairo python3-contourpy python3-cycler python3-dateutil 88s python3-decorator python3-fonttools python3-freetype python3-fs 88s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 88s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 88s python3-packaging python3-pandas python3-pandas-lib python3-pil 88s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 88s python3-reportlab python3-rlpycairo python3-scipy python3-six 88s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 88s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 88s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 88s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 88s xfonts-encodings xfonts-utils xml-core zip 88s Suggested packages: 88s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 88s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 88s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 88s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 88s t-coffee wise python-cycler-doc python-joblib-doc python-lxml-doc 88s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 88s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 88s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 88s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 88s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 88s python3-dev python3-pytest python-pandas-doc python3-statsmodels 88s python-pil-doc python-pomegranate-doc pdf-viewer python3-egenix-mxtexttools 88s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 88s python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 88s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase 88s r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray 88s r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy 88s r-bioc-deseq2 r-bioc-annotate r-cran-runit sgml-base-doc debhelper 88s Recommended packages: 88s javascript-common poppler-data python-biopython-doc ncbi-blast+ 88s python3-pytest python3-simplejson python3-psutil python3-bs4 88s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 88s python3-odf python3-openpyxl python3-tables python3-numba python3-olefile 88s fonts-dejavu-extra g++ | c++-compiler isympy-common r-recommended r-base-dev 88s r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 88s x11-utils x11-xserver-utils 88s The following NEW packages will be installed: 88s autopkgtest-satdep blt cnvkit fontconfig fontconfig-config fonts-dejavu-core 88s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 88s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 88s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 88s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 88s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 88s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 88s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 88s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 88s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 88s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 88s python3-cairo python3-contourpy python3-cycler python3-dateutil 88s python3-decorator python3-fonttools python3-freetype python3-fs 88s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 88s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 88s python3-packaging python3-pandas python3-pandas-lib python3-pil 88s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 88s python3-reportlab python3-rlpycairo python3-scipy python3-six 88s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 88s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 88s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 88s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 88s xfonts-encodings xfonts-utils xml-core zip 88s 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 162 MB/162 MB of archives. 88s After this operation, 681 MB of additional disk space will be used. 88s Get:1 /tmp/autopkgtest.oFzITZ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 89s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 89s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 89s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 89s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 89s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 89s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 89s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 89s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB] 89s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 89s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 89s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 89s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 89s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 90s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 90s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.7-3 [116 kB] 90s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.0-2 [106 kB] 90s Get:25 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-tk amd64 3.12.7-1 [9752 B] 90s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 10.4.0-1ubuntu1 [9394 B] 90s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 90s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 90s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB] 90s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 90s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 90s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu1 [184 kB] 90s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 90s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB] 90s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 90s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB] 90s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 90s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB] 90s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB] 90s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB] 90s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 90s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 90s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 90s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 10.4.0-1ubuntu1 [463 kB] 90s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 90s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 90s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 90s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 90s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2 [119 kB] 90s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 90s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 90s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.2.5-1 [1107 kB] 90s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 90s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 90s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.84+dfsg-4 [1714 kB] 90s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 90s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 90s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.2.1-1 [171 kB] 90s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-3 [2928 kB] 90s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB] 90s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 90s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.0-2 [217 kB] 90s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 90s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 90s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 90s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 90s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 91s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 91s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 91s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-1 [4228 kB] 91s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 91s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 91s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 91s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu1 [169 kB] 91s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.0-1 [1282 kB] 91s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 91s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 91s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 91s Get:79 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 91s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-2 [55.1 kB] 91s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 91s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 91s Get:83 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-3 [4545 kB] 91s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB] 91s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 91s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 91s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 92s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.14.8-6 [2549 kB] 92s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.5.0-1 [20.7 kB] 92s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 92s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-1 [132 kB] 92s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 92s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.22.1+ds-2 [3504 kB] 92s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 92s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 92s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 92s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu1 [185 kB] 92s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 92s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB] 92s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B] 92s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 92s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 92s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 92s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 92s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 92s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB] 92s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB] 92s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB] 92s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 92s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 92s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 92s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1 [28.9 MB] 94s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.50.0-2 [605 kB] 94s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.78.0-1 [378 kB] 94s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.10-2 [20.5 MB] 95s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler140 amd64 24.08.0-1 [1168 kB] 95s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 24.08.0-1 [225 kB] 95s Preconfiguring packages ... 95s Fetched 162 MB in 7s (24.6 MB/s) 95s Selecting previously unselected package sgml-base. 95s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75548 files and directories currently installed.) 95s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 95s Unpacking sgml-base (1.31) ... 95s Selecting previously unselected package libtcl8.6:amd64. 95s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... 95s Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... 95s Selecting previously unselected package fonts-dejavu-mono. 95s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 95s Unpacking fonts-dejavu-mono (2.37-8) ... 95s Selecting previously unselected package fonts-dejavu-core. 95s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 95s Unpacking fonts-dejavu-core (2.37-8) ... 95s Selecting previously unselected package libfontenc1:amd64. 95s Preparing to unpack .../004-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 95s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 95s Selecting previously unselected package x11-common. 95s Preparing to unpack .../005-x11-common_1%3a7.7+23ubuntu3_all.deb ... 95s Unpacking x11-common (1:7.7+23ubuntu3) ... 95s Selecting previously unselected package xfonts-encodings. 95s Preparing to unpack .../006-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 95s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 95s Selecting previously unselected package xfonts-utils. 95s Preparing to unpack .../007-xfonts-utils_1%3a7.7+7_amd64.deb ... 95s Unpacking xfonts-utils (1:7.7+7) ... 95s Selecting previously unselected package fonts-urw-base35. 95s Preparing to unpack .../008-fonts-urw-base35_20200910-8_all.deb ... 95s Unpacking fonts-urw-base35 (20200910-8) ... 96s Selecting previously unselected package fontconfig-config. 96s Preparing to unpack .../009-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 96s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 96s Selecting previously unselected package libfontconfig1:amd64. 96s Preparing to unpack .../010-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 96s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 96s Selecting previously unselected package libxrender1:amd64. 96s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 96s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 96s Selecting previously unselected package libxft2:amd64. 96s Preparing to unpack .../012-libxft2_2.3.6-1build1_amd64.deb ... 96s Unpacking libxft2:amd64 (2.3.6-1build1) ... 96s Selecting previously unselected package libxss1:amd64. 96s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_amd64.deb ... 96s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 96s Selecting previously unselected package libtk8.6:amd64. 96s Preparing to unpack .../014-libtk8.6_8.6.15-1_amd64.deb ... 96s Unpacking libtk8.6:amd64 (8.6.15-1) ... 96s Selecting previously unselected package tk8.6-blt2.5. 96s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 96s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 96s Selecting previously unselected package blt. 96s Preparing to unpack .../016-blt_2.5.3+dfsg-7build1_amd64.deb ... 96s Unpacking blt (2.5.3+dfsg-7build1) ... 96s Selecting previously unselected package libblas3:amd64. 96s Preparing to unpack .../017-libblas3_3.12.0-3build2_amd64.deb ... 96s Unpacking libblas3:amd64 (3.12.0-3build2) ... 96s Selecting previously unselected package libgfortran5:amd64. 96s Preparing to unpack .../018-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 96s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 96s Selecting previously unselected package liblapack3:amd64. 96s Preparing to unpack .../019-liblapack3_3.12.0-3build2_amd64.deb ... 96s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 96s Selecting previously unselected package python3-numpy. 96s Preparing to unpack .../020-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 96s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 96s Selecting previously unselected package python3.12-tk. 96s Preparing to unpack .../021-python3.12-tk_3.12.7-3_amd64.deb ... 96s Unpacking python3.12-tk (3.12.7-3) ... 96s Selecting previously unselected package python3.13-tk. 96s Preparing to unpack .../022-python3.13-tk_3.13.0-2_amd64.deb ... 96s Unpacking python3.13-tk (3.13.0-2) ... 96s Selecting previously unselected package python3-tk:amd64. 96s Preparing to unpack .../023-python3-tk_3.12.7-1_amd64.deb ... 96s Unpacking python3-tk:amd64 (3.12.7-1) ... 96s Selecting previously unselected package python3-pil.imagetk:amd64. 96s Preparing to unpack .../024-python3-pil.imagetk_10.4.0-1ubuntu1_amd64.deb ... 96s Unpacking python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 96s Selecting previously unselected package libgomp1:amd64. 96s Preparing to unpack .../025-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 96s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 96s Selecting previously unselected package libimagequant0:amd64. 96s Preparing to unpack .../026-libimagequant0_2.18.0-1build1_amd64.deb ... 96s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 96s Selecting previously unselected package libjpeg-turbo8:amd64. 96s Preparing to unpack .../027-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ... 96s Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... 96s Selecting previously unselected package libjpeg8:amd64. 96s Preparing to unpack .../028-libjpeg8_8c-2ubuntu11_amd64.deb ... 96s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 96s Selecting previously unselected package liblcms2-2:amd64. 96s Preparing to unpack .../029-liblcms2-2_2.16-2_amd64.deb ... 96s Unpacking liblcms2-2:amd64 (2.16-2) ... 96s Selecting previously unselected package libopenjp2-7:amd64. 96s Preparing to unpack .../030-libopenjp2-7_2.5.0-2ubuntu1_amd64.deb ... 96s Unpacking libopenjp2-7:amd64 (2.5.0-2ubuntu1) ... 96s Selecting previously unselected package libgraphite2-3:amd64. 96s Preparing to unpack .../031-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 96s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 96s Selecting previously unselected package libharfbuzz0b:amd64. 96s Preparing to unpack .../032-libharfbuzz0b_10.0.1-1_amd64.deb ... 96s Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... 96s Selecting previously unselected package libraqm0:amd64. 97s Preparing to unpack .../033-libraqm0_0.10.1-1build1_amd64.deb ... 97s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 97s Selecting previously unselected package libdeflate0:amd64. 97s Preparing to unpack .../034-libdeflate0_1.22-1_amd64.deb ... 97s Unpacking libdeflate0:amd64 (1.22-1) ... 97s Selecting previously unselected package libjbig0:amd64. 97s Preparing to unpack .../035-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 97s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 97s Selecting previously unselected package liblerc4:amd64. 97s Preparing to unpack .../036-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ... 97s Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ... 97s Selecting previously unselected package libsharpyuv0:amd64. 97s Preparing to unpack .../037-libsharpyuv0_1.4.0-0.1_amd64.deb ... 97s Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... 97s Selecting previously unselected package libwebp7:amd64. 97s Preparing to unpack .../038-libwebp7_1.4.0-0.1_amd64.deb ... 97s Unpacking libwebp7:amd64 (1.4.0-0.1) ... 97s Selecting previously unselected package libtiff6:amd64. 97s Preparing to unpack .../039-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 97s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 97s Selecting previously unselected package libwebpdemux2:amd64. 97s Preparing to unpack .../040-libwebpdemux2_1.4.0-0.1_amd64.deb ... 97s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 97s Selecting previously unselected package libwebpmux3:amd64. 97s Preparing to unpack .../041-libwebpmux3_1.4.0-0.1_amd64.deb ... 97s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 97s Selecting previously unselected package python3-pil:amd64. 97s Preparing to unpack .../042-python3-pil_10.4.0-1ubuntu1_amd64.deb ... 97s Unpacking python3-pil:amd64 (10.4.0-1ubuntu1) ... 97s Selecting previously unselected package libpixman-1-0:amd64. 97s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_amd64.deb ... 97s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 97s Selecting previously unselected package libxcb-render0:amd64. 97s Preparing to unpack .../044-libxcb-render0_1.17.0-2_amd64.deb ... 97s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 97s Selecting previously unselected package libxcb-shm0:amd64. 97s Preparing to unpack .../045-libxcb-shm0_1.17.0-2_amd64.deb ... 97s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 97s Selecting previously unselected package libcairo2:amd64. 97s Preparing to unpack .../046-libcairo2_1.18.2-2_amd64.deb ... 97s Unpacking libcairo2:amd64 (1.18.2-2) ... 97s Selecting previously unselected package python3-cairo. 97s Preparing to unpack .../047-python3-cairo_1.26.1-2_amd64.deb ... 97s Unpacking python3-cairo (1.26.1-2) ... 97s Selecting previously unselected package python3-freetype. 97s Preparing to unpack .../048-python3-freetype_2.5.1-1_all.deb ... 97s Unpacking python3-freetype (2.5.1-1) ... 97s Selecting previously unselected package python3-rlpycairo. 97s Preparing to unpack .../049-python3-rlpycairo_0.3.0-3_all.deb ... 97s Unpacking python3-rlpycairo (0.3.0-3) ... 97s Selecting previously unselected package python3-reportlab. 97s Preparing to unpack .../050-python3-reportlab_4.2.5-1_all.deb ... 97s Unpacking python3-reportlab (4.2.5-1) ... 97s Selecting previously unselected package xml-core. 97s Preparing to unpack .../051-xml-core_0.19_all.deb ... 97s Unpacking xml-core (0.19) ... 97s Selecting previously unselected package w3c-sgml-lib. 97s Preparing to unpack .../052-w3c-sgml-lib_1.3-3_all.deb ... 97s Unpacking w3c-sgml-lib (1.3-3) ... 97s Selecting previously unselected package python3-biopython. 97s Preparing to unpack .../053-python3-biopython_1.84+dfsg-4_amd64.deb ... 97s Unpacking python3-biopython (1.84+dfsg-4) ... 97s Selecting previously unselected package libjs-jquery. 97s Preparing to unpack .../054-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 97s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 97s Selecting previously unselected package libjs-jquery-ui. 97s Preparing to unpack .../055-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 97s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 97s Selecting previously unselected package fonts-lyx. 97s Preparing to unpack .../056-fonts-lyx_2.4.2.1-1_all.deb ... 97s Unpacking fonts-lyx (2.4.2.1-1) ... 97s Selecting previously unselected package python-matplotlib-data. 97s Preparing to unpack .../057-python-matplotlib-data_3.8.3-3_all.deb ... 97s Unpacking python-matplotlib-data (3.8.3-3) ... 97s Selecting previously unselected package python3-six. 97s Preparing to unpack .../058-python3-six_1.16.0-7_all.deb ... 97s Unpacking python3-six (1.16.0-7) ... 97s Selecting previously unselected package python3-dateutil. 97s Preparing to unpack .../059-python3-dateutil_2.9.0-2_all.deb ... 97s Unpacking python3-dateutil (2.9.0-2) ... 97s Selecting previously unselected package python3-contourpy. 97s Preparing to unpack .../060-python3-contourpy_1.3.0-2_amd64.deb ... 97s Unpacking python3-contourpy (1.3.0-2) ... 97s Selecting previously unselected package python3-cycler. 97s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 97s Unpacking python3-cycler (0.12.1-1) ... 97s Selecting previously unselected package python3-brotli. 97s Preparing to unpack .../062-python3-brotli_1.1.0-2build2_amd64.deb ... 97s Unpacking python3-brotli (1.1.0-2build2) ... 97s Selecting previously unselected package python3-decorator. 97s Preparing to unpack .../063-python3-decorator_5.1.1-5_all.deb ... 97s Unpacking python3-decorator (5.1.1-5) ... 97s Selecting previously unselected package liblbfgsb0:amd64. 97s Preparing to unpack .../064-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 97s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 97s Selecting previously unselected package python3-scipy. 98s Preparing to unpack .../065-python3-scipy_1.13.1-5_amd64.deb ... 98s Unpacking python3-scipy (1.13.1-5) ... 98s Selecting previously unselected package python3-ufolib2. 98s Preparing to unpack .../066-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 98s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 98s Selecting previously unselected package python3-mpmath. 98s Preparing to unpack .../067-python3-mpmath_1.3.0-1_all.deb ... 98s Unpacking python3-mpmath (1.3.0-1) ... 98s Selecting previously unselected package python3-sympy. 98s Preparing to unpack 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Setting up libxcb-shm0:amd64 (1.17.0-2) ... 103s Setting up libpaper-utils (1.1.29build1) ... 103s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 103s Setting up python3-freetype (2.5.1-1) ... 103s Setting up python3-networkx (3.2.1-4ubuntu1) ... 104s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 104s Setting up python3-tz (2024.1-2) ... 104s Setting up unicode-data (15.1.0-1) ... 104s Setting up python3-six (1.16.0-7) ... 104s Setting up python3-decorator (5.1.1-5) ... 104s Setting up zip (3.0-14ubuntu1) ... 104s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 104s Setting up libblas3:amd64 (3.12.0-3build2) ... 104s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 104s Setting up python3-packaging (24.1-1) ... 104s Setting up python3-brotli (1.1.0-2build2) ... 105s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 105s Setting up python3-cycler (0.12.1-1) ... 105s 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(1.4.0-0.1) ... 105s Setting up python3-appdirs (1.4.4-4) ... 105s Setting up xdg-utils (1.2.1-0ubuntu1) ... 105s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 105s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 105s Setting up python3-pyfaidx (0.8.1.3-1) ... 105s Setting up python3-sympy (1.13.3-1) ... 110s Setting up libice6:amd64 (2:1.1.1-1) ... 110s Setting up liblapack3:amd64 (3.12.0-3build2) ... 110s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 110s Setting up python3-pysam (0.22.1+ds-2) ... 110s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 111s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 111s Setting up xfonts-utils (1:7.7+7) ... 111s Setting up python3-fs (2.4.16-4) ... 111s Setting up libthai0:amd64 (0.1.29-2build1) ... 111s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 111s Setting up libraqm0:amd64 (0.10.1-1build1) ... 111s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 112s Setting up python3-lxml:amd64 (5.3.0-1) ... 112s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 112s Setting up xml-core (0.19) ... 112s Setting up python3-contourpy (1.3.0-2) ... 113s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 113s Setting up libsm6:amd64 (2:1.2.4-1) ... 113s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 113s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 115s Regenerating fonts cache... done. 115s Setting up libxft2:amd64 (2.3.6-1build1) ... 115s Setting up python3-scipy (1.13.1-5) ... 117s Setting up python3-pomegranate (0.14.8-6) ... 118s Setting up libtk8.6:amd64 (8.6.15-1) ... 118s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ... 118s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... 118s Setting up python3.12-tk (3.12.7-3) ... 118s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 118s Setting up fonts-urw-base35 (20200910-8) ... 118s Setting up libcairo2:amd64 (1.18.2-2) ... 118s Setting up python3.13-tk (3.13.0-2) ... 118s Setting up python3-pil:amd64 (10.4.0-1ubuntu1) ... 118s Setting up python3-pandas (2.2.3+dfsg-5) ... 122s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 122s Setting up python3-sklearn (1.4.2+dfsg-6) ... 123s Setting up libpoppler140:amd64 (24.08.0-1) ... 123s Setting up poppler-utils (24.08.0-1) ... 123s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... 123s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... 123s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 123s Setting up python3-cairo (1.26.1-2) ... 123s Setting up blt (2.5.3+dfsg-7build1) ... 123s Setting up python3-tk:amd64 (3.12.7-1) ... 123s Setting up python3-pil.imagetk:amd64 (10.4.0-1ubuntu1) ... 123s Setting up python3-rlpycairo (0.3.0-3) ... 124s Setting up r-base-core (4.4.2-1) ... 124s 124s Creating config file /etc/R/Renviron with new version 124s Setting up python3-reportlab (4.2.5-1) ... 124s Setting up r-bioc-biocgenerics (0.50.0-2) ... 124s Setting up r-bioc-dnacopy (1.78.0-1) ... 124s Setting up python3-fonttools (4.46.0-1build2) ... 125s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 125s Setting up python3-matplotlib (3.8.3-3) ... 126s Processing triggers for libc-bin (2.40-1ubuntu3) ... 126s Processing triggers for man-db (2.12.1-3) ... 127s Processing triggers for install-info (7.1.1-1) ... 127s Processing triggers for sgml-base (1.31) ... 127s Setting up w3c-sgml-lib (1.3-3) ... 151s Setting up python3-biopython (1.84+dfsg-4) ... 152s Setting up cnvkit (0.9.10-2) ... 152s Setting up autopkgtest-satdep (0) ... 156s (Reading database ... 92809 files and directories currently installed.) 156s Removing autopkgtest-satdep (0) ... 156s autopkgtest [08:14:33]: test run-unit-test: [----------------------- 157s 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/ 159s Created directory build/ 159s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 159s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 159s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 159s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 159s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 159s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 159s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 159s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 159s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 160s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 161s Number of target and antitarget files: 3, 3 161s No FASTA reference genome provided; skipping GC, RM calculations 161s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 161s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 161s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 161s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 161s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 161s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 161s Loading build/p2-20_5.targetcoverage.cnn 161s Correcting for GC bias... 161s Correcting for density bias... 161s Loading build/p2-5_5.targetcoverage.cnn 161s Correcting for GC bias... 161s Correcting for density bias... 161s Loading build/p2-9_5.targetcoverage.cnn 161s Correcting for GC bias... 161s Correcting for density bias... 161s Loading build/p2-20_5.antitargetcoverage.cnn 161s Correcting for GC bias... 161s Loading build/p2-5_5.antitargetcoverage.cnn 161s Correcting for GC bias... 162s Loading build/p2-9_5.antitargetcoverage.cnn 162s Correcting for GC bias... 162s Calculating average bin coverages 167s Calculating bin spreads 168s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 168s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 168s " chr1:2435319-2436685 log2=-0.709 spread=0.503 168s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 168s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 168s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 168s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 168s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 168s " chr1:120611883-120612051 log2=0.070 spread=0.050 168s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 168s " chr1:156842391-156842479 log2=-0.398 spread=0.290 168s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 168s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 168s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 168s " chr1:183481886-183481951 log2=-0.040 spread=0.119 168s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 168s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 168s " chr1:243800859-243801066 log2=0.023 spread=0.063 168s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 168s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 168s " chr2:25536716-25536891 log2=0.702 spread=0.033 168s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 168s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 168s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 168s REL chr2:61108881-61109061 log2=1.026 spread=0.559 168s " chr2:61128072-61128256 log2=0.115 spread=0.173 168s " chr2:61145275-61145462 log2=0.014 spread=0.099 168s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 168s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 168s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 168s " chr2:128095237-128095425 log2=0.215 spread=0.212 168s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 168s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 168s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 168s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 168s " chr3:97160189-97160367 log2=-0.050 spread=0.191 168s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 168s " chr3:142286854-142287031 log2=-0.076 spread=0.116 168s GAK chr4:896278-896357 log2=-1.505 spread=1.261 168s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 168s " chr4:1803044-1803507 log2=-0.073 spread=0.117 168s " chr4:1808792-1809022 log2=0.252 spread=0.108 168s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 168s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 168s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 168s " chr4:178514600-178514725 log2=-0.098 spread=0.096 168s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 168s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 168s " chr5:1295312-1295381 log2=-0.690 spread=0.462 168s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 168s " chr5:25519857-25520034 log2=-0.015 spread=0.095 168s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 168s " chr5:38962338-38962525 log2=0.005 spread=0.019 168s " chr5:38966685-38966862 log2=0.006 spread=0.165 168s " chr5:38978620-38978763 log2=0.040 spread=0.030 168s " chr5:39074133-39074327 log2=-0.158 spread=0.139 168s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 168s " chr5:51030131-51030313 log2=-0.034 spread=0.192 168s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 168s " chr5:56168412-56168590 log2=0.479 spread=0.038 168s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 168s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 168s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 168s " chr5:86637023-86637168 log2=0.054 spread=0.111 168s " chr5:86642414-86642592 log2=0.254 spread=0.162 168s " chr5:86648912-86649096 log2=0.092 spread=0.062 168s " chr5:86670598-86670778 log2=0.222 spread=0.198 168s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 168s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 168s APC chr5:112101965-112102138 log2=0.104 spread=0.217 168s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 168s " chr5:170837567-170837631 log2=0.085 spread=0.349 168s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 168s " chr5:180046203-180046404 log2=-1.531 spread=0.722 168s " chr5:180076418-180076603 log2=-2.224 spread=1.416 168s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 168s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 168s " chr6:31939599-31940313 log2=-19.582 spread=0.181 168s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 168s " chr6:31946632-31946824 log2=-20.052 spread=0.088 168s " chr6:31947142-31947366 log2=-20.114 spread=0.066 168s " chr6:31948176-31948360 log2=-19.982 spread=0.149 168s " chr6:31948382-31948612 log2=-19.757 spread=0.165 168s " chr6:31948730-31949253 log2=-20.048 spread=0.014 168s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 168s " chr6:32164046-32164227 log2=-19.755 spread=0.189 168s " chr6:32164652-32164888 log2=-19.984 spread=0.154 168s " chr6:32165021-32165403 log2=-19.625 spread=0.196 168s " chr6:32166163-32166545 log2=-20.043 spread=0.072 168s " chr6:32166648-32166962 log2=-3.514 spread=5.742 168s " chr6:32168554-32168821 log2=-19.601 spread=0.197 168s " chr6:32168844-32169306 log2=-19.683 spread=0.166 168s " chr6:32169801-32170391 log2=-19.405 spread=0.205 168s " chr6:32171492-32171691 log2=-20.095 spread=0.101 168s " chr6:32171861-32172198 log2=-3.141 spread=7.288 168s " chr6:32178478-32178749 log2=-19.927 spread=0.164 168s " chr6:32180197-32180441 log2=-10.902 spread=9.532 168s " chr6:32180544-32180722 log2=-19.675 spread=0.186 168s " chr6:32180857-32181062 log2=-19.562 spread=0.227 168s " chr6:32181411-32181646 log2=-19.966 spread=0.171 168s " chr6:32181832-32182066 log2=-19.961 spread=0.172 168s " chr6:32182948-32183194 log2=-19.935 spread=0.168 168s " chr6:32184667-32185079 log2=-19.923 spread=0.165 168s " chr6:32185720-32185919 log2=-19.707 spread=0.197 168s " chr6:32187317-32187601 log2=-19.765 spread=0.173 168s " chr6:32187871-32188094 log2=-19.660 spread=0.188 168s " chr6:32188127-32188451 log2=-19.622 spread=0.169 168s " chr6:32188481-32188693 log2=-19.902 spread=0.132 168s " chr6:32188704-32189133 log2=-19.501 spread=0.193 168s " chr6:32190258-32190616 log2=-19.570 spread=0.209 168s " chr6:32190724-32190908 log2=-19.540 spread=0.232 168s " chr6:32191570-32191668 log2=-19.773 spread=0.178 168s " chr6:32191676-32191753 log2=-19.374 spread=0.201 168s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 168s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 168s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 168s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 168s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 168s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 168s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 168s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 168s " chr6:128316545-128316699 log2=-0.070 spread=0.050 168s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 168s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 168s " chr6:157099442-157099991 log2=-0.846 spread=0.504 168s " chr6:157100042-157100634 log2=-1.570 spread=0.825 168s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 168s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 168s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 168s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 168s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 168s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 168s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 168s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 168s " chr7:98491365-98491541 log2=0.209 spread=0.153 168s " chr7:98493314-98493496 log2=0.389 spread=0.207 168s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 168s " chr7:128829048-128829358 log2=-0.474 spread=0.315 168s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 168s " chr7:140484736-140484912 log2=0.081 spread=0.150 168s " chr7:140487956-140488430 log2=-0.089 spread=0.142 168s " chr7:140493336-140493442 log2=-0.340 spread=0.283 168s " chr7:140624315-140624540 log2=-0.497 spread=0.342 168s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 168s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 168s " chr8:30941153-30941335 log2=0.079 spread=0.294 168s " chr8:30942625-30942802 log2=0.044 spread=0.247 168s " chr8:30947918-30948092 log2=0.151 spread=0.124 168s " chr8:31000128-31000252 log2=-0.099 spread=0.098 168s " chr8:31001006-31001182 log2=-0.002 spread=0.062 168s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 168s " chr8:37698557-37699898 log2=-0.612 spread=0.029 168s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 168s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 168s " chr8:48845528-48845758 log2=0.056 spread=0.196 168s " chr8:48866846-48867043 log2=-0.067 spread=0.097 168s " chr8:48868369-48868526 log2=-0.239 spread=0.174 168s " chr8:48872485-48872722 log2=-0.636 spread=0.464 168s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 168s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 168s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 168s " chr9:2101491-2101640 log2=0.244 spread=0.104 168s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 168s " chr9:5067014-5067883 log2=0.146 spread=0.089 168s " chr9:5068184-5070306 log2=0.133 spread=0.092 168s " chr9:5076944-5077152 log2=0.046 spread=0.137 168s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 168s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 168s " chr9:21986759-21986899 log2=0.058 spread=0.175 168s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 168s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 168s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 168s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 168s " chr9:87425375-87425452 log2=0.494 spread=0.066 168s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 168s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 168s " chr9:139250747-139251032 log2=-0.223 spread=0.273 168s " chr9:139252418-139252703 log2=-0.512 spread=0.264 168s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 168s " chr9:139417262-139417677 log2=-0.173 spread=0.191 168s " chr9:139440110-139440287 log2=-1.257 spread=0.500 168s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 168s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 168s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 168s " chr10:43600360-43600677 log2=-0.341 spread=0.222 168s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 168s " chr10:89685254-89685374 log2=0.244 spread=0.259 168s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 168s " chr10:93579008-93579121 log2=0.166 spread=0.220 168s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 168s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 168s " chr10:112679716-112679934 log2=-0.008 spread=0.028 168s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 168s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 168s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 168s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 168s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 168s " chr11:94170270-94170454 log2=0.095 spread=0.285 168s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 168s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 168s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 168s " chr11:108164020-108164234 log2=-0.056 spread=0.040 168s " chr11:108217986-108218135 log2=0.359 spread=0.277 168s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 168s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 168s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 168s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 168s " chr12:25391004-25391186 log2=0.368 spread=0.128 168s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 168s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 168s " chr12:51206782-51207287 log2=-0.012 spread=0.101 168s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 168s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 168s " chr13:26970356-26970536 log2=0.137 spread=0.121 168s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 168s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 168s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 168s " chr13:32903506-32903689 log2=0.019 spread=0.232 168s " chr13:32918645-32918823 log2=0.158 spread=0.114 168s " chr13:32920899-32921077 log2=0.014 spread=0.247 168s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 168s " chr13:48919164-48919369 log2=0.025 spread=0.094 168s " chr13:48921877-48922044 log2=0.106 spread=0.147 168s " chr13:48923026-48923204 log2=0.360 spread=0.016 168s " chr13:48938965-48939147 log2=0.084 spread=0.356 168s " chr13:48941578-48941767 log2=0.238 spread=0.212 168s " chr13:48947486-48947665 log2=0.025 spread=0.126 168s " chr13:48954166-48954251 log2=0.061 spread=0.273 168s " chr13:49037815-49038005 log2=0.063 spread=0.062 168s " chr13:49047410-49047589 log2=0.053 spread=0.170 168s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 168s " chr13:85527771-85527948 log2=0.007 spread=0.222 168s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 168s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 168s " chr13:110438332-110438432 log2=-3.643 spread=2.325 168s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 168s " chr14:20291466-20291612 log2=0.697 spread=0.248 168s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 168s " chr14:36989195-36989373 log2=0.023 spread=0.162 168s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 168s " chr14:50619741-50619923 log2=0.003 spread=0.272 168s " chr14:50697856-50698044 log2=0.277 spread=0.334 168s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 168s " chr14:71275790-71275923 log2=-2.815 spread=1.938 168s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 168s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 168s " chr15:38544477-38545455 log2=-0.348 spread=0.179 168s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 168s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 168s " chr15:41803968-41804185 log2=-2.202 spread=0.188 168s " chr15:41804261-41804494 log2=-0.402 spread=0.392 168s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 168s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 168s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 168s " chr16:2611404-2611585 log2=-5.171 spread=1.963 168s " chr16:2611721-2611943 log2=-11.810 spread=9.172 168s " chr16:2615504-2615725 log2=-20.113 spread=0.007 168s " chr16:2616307-2616486 log2=-20.054 spread=0.072 168s " chr16:2631267-2631414 log2=-20.009 spread=0.061 168s " chr16:2631583-2631734 log2=-20.089 spread=0.090 168s " chr16:2633363-2633616 log2=-20.101 spread=0.089 168s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 168s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 168s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 168s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 168s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 168s " chr16:50826460-50826650 log2=0.239 spread=0.204 168s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 168s " chr16:60005694-60005857 log2=-0.366 spread=0.298 168s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 168s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 168s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 168s " chr17:12011053-12011253 log2=0.028 spread=0.232 168s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 168s " chr17:29496854-29497046 log2=0.226 spread=0.193 168s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 168s " chr17:30519172-30519355 log2=0.163 spread=0.289 168s " chr17:30525911-30526093 log2=-0.157 spread=0.046 168s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 168s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 168s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 168s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 168s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 168s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 168s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 168s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 168s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 168s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 168s " chr19:2210351-2210545 log2=-0.860 spread=0.261 168s " chr19:2226130-2227152 log2=-0.113 spread=0.120 168s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 168s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 168s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 168s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 168s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 168s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 168s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 168s " chr19:15311544-15311749 log2=-1.887 spread=1.202 168s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 168s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 168s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 168s " chr19:33792774-33793010 log2=-1.781 spread=0.127 168s " chr19:33793014-33793356 log2=-0.541 spread=0.385 168s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 168s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 168s " chr19:45873698-45873881 log2=-0.522 spread=0.327 168s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 168s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 168s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 168s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 168s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 168s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 168s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 168s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 168s " chr21:36265140-36265318 log2=0.042 spread=0.039 168s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 168s " chr22:29115325-29115465 log2=0.055 spread=0.390 168s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 168s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 168s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 168s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 168s " chrX:1317372-1317594 log2=-21.121 spread=0.049 168s " chrX:1321225-1321435 log2=-20.851 spread=0.196 168s " chrX:1325274-1325530 log2=-21.121 spread=0.011 168s " chrX:1327651-1327830 log2=-21.000 spread=0.029 168s " chrX:1331391-1331576 log2=-21.018 spread=0.052 168s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 168s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 168s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 168s " chrX:123185143-123185290 log2=-1.018 spread=0.062 168s " chrX:123202378-123202544 log2=-0.959 spread=0.103 168s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 168s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 168s " chrY:9008607-9008759 log2=-1.012 spread=0.097 168s " chrY:13131970-13132039 log2=-1.004 spread=0.074 168s " chrY:19506485-19506650 log2=-1.018 spread=0.034 168s " chrY:21033918-21034071 log2=-1.013 spread=0.057 168s " chrY:28463435-28463622 log2=-0.952 spread=0.039 168s " chrY:28514033-28514208 log2=-0.992 spread=0.026 168s Antitargets: 108 (0.8597%) bins failed filters 168s Wrote build/reference-picard.cnn with 19209 regions 169s 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 170s Processing target: p2-5_5 170s Keeping 6308 of 6646 bins 170s Correcting for GC bias... 170s Correcting for density bias... 170s Processing antitarget: p2-5_5 170s Keeping 12455 of 12563 bins 170s Correcting for GC bias... 170s WARNING: Skipping correction for RepeatMasker bias 170s Targets are 1.18 x more variable than antitargets 170s Wrote build/p2-5_5.cnr with 18763 regions 170s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 171s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 171s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 172s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 173s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 173s 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 174s Processing target: p2-9_2 175s Keeping 6308 of 6646 bins 175s Correcting for GC bias... 175s Correcting for density bias... 175s Processing antitarget: p2-9_2 175s Keeping 12455 of 12563 bins 175s Correcting for GC bias... 175s WARNING: Skipping correction for RepeatMasker bias 175s Targets are 1.72 x more variable than antitargets 175s Wrote build/p2-9_2.cnr with 18763 regions 175s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 176s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 176s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 177s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 178s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 178s 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 179s Processing target: p2-20_1 179s Keeping 6308 of 6646 bins 179s Correcting for GC bias... 179s Correcting for density bias... 179s Processing antitarget: p2-20_1 180s Keeping 12455 of 12563 bins 180s Correcting for GC bias... 180s WARNING: Skipping correction for RepeatMasker bias 180s Targets are 1.12 x more variable than antitargets 180s Wrote build/p2-20_1.cnr with 18763 regions 180s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 181s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 181s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 181s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 183s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 183s 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 184s Processing target: p2-20_2 184s Keeping 6308 of 6646 bins 184s Correcting for GC bias... 184s Correcting for density bias... 184s Processing antitarget: p2-20_2 185s Keeping 12455 of 12563 bins 185s Correcting for GC bias... 185s WARNING: Skipping correction for RepeatMasker bias 185s Targets are 1.10 x more variable than antitargets 185s Wrote build/p2-20_2.cnr with 18763 regions 185s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 186s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 186s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 186s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 188s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 188s 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 189s Processing target: p2-20_3 189s Keeping 6308 of 6646 bins 189s Correcting for GC bias... 189s Correcting for density bias... 189s Processing antitarget: p2-20_3 189s Keeping 12455 of 12563 bins 189s Correcting for GC bias... 189s WARNING: Skipping correction for RepeatMasker bias 189s Antitargets are 1.09 x more variable than targets 190s Wrote build/p2-20_3.cnr with 18763 regions 190s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 191s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 191s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 191s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 192s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 193s 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 194s Processing target: p2-20_4 194s Keeping 6308 of 6646 bins 194s Correcting for GC bias... 194s Correcting for density bias... 194s Processing antitarget: p2-20_4 194s Keeping 12455 of 12563 bins 194s Correcting for GC bias... 194s WARNING: Skipping correction for RepeatMasker bias 194s Targets are 1.43 x more variable than antitargets 194s Wrote build/p2-20_4.cnr with 18763 regions 195s 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 196s Processing target: p2-20_5 196s Keeping 6308 of 6646 bins 196s Correcting for GC bias... 196s Correcting for density bias... 196s Processing antitarget: p2-20_5 196s Keeping 12455 of 12563 bins 196s Correcting for GC bias... 196s WARNING: Skipping correction for RepeatMasker bias 196s Targets are 2.50 x more variable than antitargets 197s Wrote build/p2-20_5.cnr with 18763 regions 197s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 198s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 203s Dropped 8 / 49 bins on chromosome chrY 203s Wrote build/p2-5_5.cns with 71 regions 204s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 205s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 206s Dropped 1 / 949 bins on chromosome chr6 210s Dropped 27 / 49 bins on chromosome chrY 210s Wrote build/p2-9_2.cns with 103 regions 210s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 212s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 217s Dropped 6 / 49 bins on chromosome chrY 217s Wrote build/p2-20_1.cns with 121 regions 218s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 219s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 225s Dropped 7 / 49 bins on chromosome chrY 225s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 225s Wrote build/p2-20_2.cns with 117 regions 226s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 231s Dropped 11 / 49 bins on chromosome chrY 231s Wrote build/p2-20_3.cns with 64 regions 231s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 233s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 238s Dropped 8 / 49 bins on chromosome chrY 238s Wrote build/p2-20_4.cns with 143 regions 239s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 240s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 245s Smoothing overshot at 1 / 123 indices: (-0.30060035404086805, 0.32508880185194927) vs. original (-0.363302, 0.311218) 245s Dropped 6 / 49 bins on chromosome chrY 246s Wrote build/p2-20_5.cns with 120 regions 246s 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 248s Wrote p2-5_5-scatter.pdf 248s 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 250s Smoothing overshot at 3 / 97 indices: (-19.900105868621722, -3.309906922372052) vs. original (-19.294, -0.16431) 250s Wrote p2-9_2-scatter.pdf 251s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 252s Showing 1480 probes and 0 selected genes in region chr1 252s Wrote p2-9_2-chr1-scatter.pdf 252s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 254s Showing 201 probes and 0 selected genes in region chr21 254s Wrote p2-9_2-chr21-scatter.pdf 254s 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 255s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 255s Wrote p2-9_2-chr9p-scatter.pdf 255s 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 257s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 257s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 257s 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 258s Detected file format: bed 258s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 258s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 258s 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 258s /usr/bin/pdfunite 259s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 260s Treating sample p2-5_5 as female 267s Wrote p2-5_5-diagram.pdf 267s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 268s Treating sample p2-9_2 as female 275s Wrote p2-9_2-diagram.pdf 275s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 276s Treating sample p2-20_1 as female 283s Wrote p2-20_1-diagram.pdf 283s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 284s Treating sample p2-20_2 as female 291s Wrote p2-20_2-diagram.pdf 291s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 292s Treating sample p2-5_5 as female 293s Wrote p2-5_5-cbs-diagram.pdf 293s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 294s Treating sample p2-9_2 as female 294s Wrote p2-9_2-cbs-diagram.pdf 294s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 295s Treating sample p2-20_1 as female 295s Wrote p2-20_1-cbs-diagram.pdf 296s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 297s Treating sample p2-20_2 as female 297s Wrote p2-20_2-cbs-diagram.pdf 297s 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 298s Treating sample p2-5_5 as female 303s Wrote p2-5_5-both-diagram.pdf 303s 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 304s Treating sample p2-9_2 as female 308s Wrote p2-9_2-both-diagram.pdf 309s 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 310s Treating sample p2-20_1 as female 314s Wrote p2-20_1-both-diagram.pdf 314s 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 315s Treating sample p2-20_2 as female 320s Wrote p2-20_2-both-diagram.pdf 320s 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 320s /usr/bin/pdfunite 320s 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 321s Treating sample p2-5_5 as female 321s Treating sample p2-9_2 as female 321s Treating sample p2-20_1 as female 321s Treating sample p2-20_2 as female 321s Treating sample p2-20_3 as female 321s Treating sample p2-20_4 as female 321s Treating sample p2-20_5 as female 323s Wrote heatmap-picard.pdf 323s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 324s Found 14 gene breakpoints 324s Wrote p2-9_2-breaks.txt 324s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 326s Treating sample p2-9_2 as female 327s Found 323 gene-level gains and losses 327s Wrote p2-9_2-genemetrics.txt 327s 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 328s Wrote gender-picard.txt 328s 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 331s Wrote p2-all.cdt 332s 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 335s Wrote p2-all-jtv.txt 335s 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 337s Wrote p2-all.seg 337s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 338s Wrote p2-9_2.nexus 338s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 339s Selected test sample NA12882 and control sample NA12878 339s Loaded 3654 records; skipped: 514 somatic, 394 depth 339s Kept 2631 heterozygous of 3654 VCF records 341s Placed 705 variants into 18763 bins 341s Wrote p2-9_2.nexus-ogt 342s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 343s Treating sample p2-5_5 as female 343s Rescaling sample with purity 0.65, ploidy 2 343s Wrote build/p2-5_5.call.cns with 71 regions 343s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 344s Treating sample p2-9_2 as female 344s Rescaling sample with purity 0.65, ploidy 2 344s Wrote build/p2-9_2.call.cns with 103 regions 344s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 345s Treating sample p2-20_1 as female 345s Rescaling sample with purity 0.65, ploidy 2 345s Wrote build/p2-20_1.call.cns with 121 regions 346s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 347s Treating sample p2-20_2 as female 347s Rescaling sample with purity 0.65, ploidy 2 347s Wrote build/p2-20_2.call.cns with 117 regions 347s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 348s Treating sample p2-20_3 as female 348s Rescaling sample with purity 0.65, ploidy 2 348s Wrote build/p2-20_3.call.cns with 64 regions 348s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 350s Treating sample p2-20_4 as female 350s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 350s Rescaling sample with purity 0.65, ploidy 2 350s Wrote build/p2-20_4.call.cns with 143 regions 351s Treating sample p2-20_5 as female 351s Rescaling sample with purity 0.65, ploidy 2 351s Wrote build/p2-20_5.call.cns with 120 regions 351s 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 352s Treating sample p2-5_5.call as female 352s Treating sample p2-9_2.call as female 352s Treating sample p2-20_1.call as female 352s Treating sample p2-20_2.call as female 352s Treating sample p2-20_3.call as female 352s Treating sample p2-20_4.call as female 352s Treating sample p2-20_5.call as female 352s Wrote p2-all.bed 352s 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 354s Treating sample p2-9_2.call as female 354s Wrote p2-9_2.vcf 354s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 355s /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)` 355s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 355s Wrote p2-9_2.theta2.input 355s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 355s --mean --median --mode --t-test \ 355s --stdev --mad --mse --iqr --bivar \ 355s --ci --pi --sem --smooth-bootstrap 357s Wrote p2-9_2-segmetrics.cns with 103 regions 357s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 357s --ci -b 50 -a 0.5 359s Wrote p2-5_5-segmetrics.cns with 71 regions 359s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 360s Wrote p2-5_5-metrics.tsv 360s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 361s Wrote p2-9_2-metrics.tsv 362s 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 363s Wrote p2-20-metrics.tsv 363s PASS 364s autopkgtest [08:18:01]: test run-unit-test: -----------------------] 364s run-unit-test PASS 364s autopkgtest [08:18:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 365s autopkgtest [08:18:02]: test pybuild-autopkgtest: preparing testbed 372s Reading package lists... 373s Building dependency tree... 373s Reading state information... 373s Starting pkgProblemResolver with broken count: 0 373s Starting 2 pkgProblemResolver with broken count: 0 373s Done 373s The following additional packages will be installed: 373s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 373s cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 373s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 373s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 373s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 373s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 373s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 373s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libquadmath0 373s libstdc++-14-dev libtool libtsan2 libubsan1 m4 po-debconf 373s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python3-all 373s python3-build python3-iniconfig python3-installer python3-pluggy 373s python3-pyproject-hooks python3-pytest python3-toml python3-wheel python3.13 373s python3.13-minimal 373s Suggested packages: 373s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 373s cpp-14-doc dh-make flit g++-multilib g++-14-multilib gcc-14-doc gcc-multilib 373s manpages-dev flex bison gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu 373s gettext-doc libasprintf-dev libgettextpo-dev libstdc++-14-doc libtool-doc 373s gfortran | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-pip 373s python3-venv python-build-doc python-installer-doc python3.13-venv 373s python3.13-doc binfmt-support 373s Recommended packages: 373s libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 373s The following NEW packages will be installed: 373s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 373s cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 373s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 373s g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 373s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 373s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 373s libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0 libisl23 libitm1 373s liblsan0 libmpc3 libpython3.13-minimal libpython3.13-stdlib libquadmath0 373s libstdc++-14-dev libtool libtsan2 libubsan1 m4 po-debconf 373s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python3-all 373s python3-build python3-iniconfig python3-installer python3-pluggy 373s python3-pyproject-hooks python3-pytest python3-toml python3-wheel python3.13 373s python3.13-minimal 373s 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 373s Need to get 76.2 MB/76.2 MB of archives. 373s After this operation, 259 MB of additional disk space will be used. 373s Get:1 /tmp/autopkgtest.oFzITZ/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [860 B] 374s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 374s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 375s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-4build1 [244 kB] 375s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3 [382 kB] 375s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 375s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 376s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.22.5-2 [616 kB] 376s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 377s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 377s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 380s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 380s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 380s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 380s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 380s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 380s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 380s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 381s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 383s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 383s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 383s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 383s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 384s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 389s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 389s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 389s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 389s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 389s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 392s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 392s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 392s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 392s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 392s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 392s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.4.7-7build1 [166 kB] 392s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 392s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 392s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 392s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 392s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-1 [46.9 kB] 392s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 392s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.22.5-2 [948 kB] 392s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 392s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 392s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.20ubuntu1 [893 kB] 392s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20241024 [112 kB] 392s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 393s Get:48 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 393s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 393s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 393s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.44.0-1 [54.2 kB] 393s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 393s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 393s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20241024 [1728 B] 393s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 393s Get:56 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 393s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 393s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 393s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 393s Fetched 76.2 MB in 20s (3827 kB/s) 393s Selecting previously unselected package libpython3.13-minimal:amd64. 393s (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 ... 92809 files and directories currently installed.) 393s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 393s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 393s Selecting previously unselected package python3.13-minimal. 393s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 393s Unpacking python3.13-minimal (3.13.0-2) ... 394s Selecting previously unselected package m4. 394s Preparing to unpack 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pybuild-autopkgtest 403s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.oFzITZ/build.sYg/src/data /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/data; 403s I: pybuild base:311: cd /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build; python3.13 -m pytest test 404s ============================= test session starts ============================== 404s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 404s rootdir: /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build 404s configfile: pyproject.toml 404s plugins: typeguard-4.4.1 404s collected 0 items / 5 errors 404s 404s ==================================== ERRORS ==================================== 404s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 404s ImportError while importing test module '/tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/test/test_cnvlib.py'. 404s Hint: make sure your test modules/packages have valid Python names. 404s Traceback: 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 404s from . import multiarray 404s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 404s from . import overrides 404s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 404s from numpy.core._multiarray_umath import ( 404s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 404s 404s During handling of the above exception, another exception occurred: 404s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 404s from numpy.__config__ import show as show_config 404s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 404s from numpy.core._multiarray_umath import ( 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 404s raise ImportError(msg) 404s E ImportError: 404s E 404s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 404s E 404s E Importing the numpy C-extensions failed. This error can happen for 404s E many reasons, often due to issues with your setup or how NumPy was 404s E installed. 404s E 404s E We have compiled some common reasons and troubleshooting tips at: 404s E 404s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 404s E 404s E Please note and check the following: 404s E 404s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 404s E * The NumPy version is: "1.26.4" 404s E 404s E and make sure that they are the versions you expect. 404s E Please carefully study the documentation linked above for further help. 404s E 404s E Original error was: No module named 'numpy.core._multiarray_umath' 404s 404s The above exception was the direct cause of the following exception: 404s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 404s return _bootstrap._gcd_import(name[level:], package, level) 404s test/test_cnvlib.py:15: in 404s import numpy as np 404s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 404s raise ImportError(msg) from e 404s E ImportError: Error importing numpy: you should not try to import numpy from 404s E its source directory; please exit the numpy source tree, and relaunch 404s E your python interpreter from there. 404s ____________________ ERROR collecting test/test_commands.py ____________________ 404s ImportError while importing test module '/tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/test/test_commands.py'. 404s Hint: make sure your test modules/packages have valid Python names. 404s Traceback: 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 404s from . import multiarray 404s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 404s from . import overrides 404s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 404s from numpy.core._multiarray_umath import ( 404s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 404s 404s During handling of the above exception, another exception occurred: 404s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 404s from numpy.__config__ import show as show_config 404s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 404s from numpy.core._multiarray_umath import ( 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 404s raise ImportError(msg) 404s E ImportError: 404s E 404s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 404s E 404s E Importing the numpy C-extensions failed. This error can happen for 404s E many reasons, often due to issues with your setup or how NumPy was 404s E installed. 404s E 404s E We have compiled some common reasons and troubleshooting tips at: 404s E 404s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 404s E 404s E Please note and check the following: 404s E 404s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 404s E * The NumPy version is: "1.26.4" 404s E 404s E and make sure that they are the versions you expect. 404s E Please carefully study the documentation linked above for further help. 404s E 404s E Original error was: No module named 'numpy.core._multiarray_umath' 404s 404s The above exception was the direct cause of the following exception: 404s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 404s return _bootstrap._gcd_import(name[level:], package, level) 404s test/test_commands.py:16: in 404s import numpy as np 404s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 404s raise ImportError(msg) from e 404s E ImportError: Error importing numpy: you should not try to import numpy from 404s E its source directory; please exit the numpy source tree, and relaunch 404s E your python interpreter from there. 404s _____________________ ERROR collecting test/test_genome.py _____________________ 404s ImportError while importing test module '/tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/test/test_genome.py'. 404s Hint: make sure your test modules/packages have valid Python names. 404s Traceback: 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 404s from . import multiarray 404s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 404s from . import overrides 404s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 404s from numpy.core._multiarray_umath import ( 404s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 404s 404s During handling of the above exception, another exception occurred: 404s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 404s from numpy.__config__ import show as show_config 404s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 404s from numpy.core._multiarray_umath import ( 404s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 404s raise ImportError(msg) 404s E ImportError: 404s E 404s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 404s E 404s E Importing the numpy C-extensions failed. This error can happen for 404s E many reasons, often due to issues with your setup or how NumPy was 404s E installed. 404s E 404s E We have compiled some common reasons and troubleshooting tips at: 404s E 404s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 404s E 404s E Please note and check the following: 404s E 404s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 404s E * The NumPy version is: "1.26.4" 404s E 404s E and make sure that they are the versions you expect. 404s E Please carefully study the documentation linked above for further help. 404s E 404s E Original error was: No module named 'numpy.core._multiarray_umath' 404s 404s The above exception was the direct cause of the following exception: 404s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 404s return _bootstrap._gcd_import(name[level:], package, level) 404s test/test_genome.py:12: in 404s import numpy as np 404s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 404s raise ImportError(msg) from e 404s E ImportError: Error importing numpy: you should not try to import numpy from 404s E its source directory; please exit the numpy source tree, and relaunch 404s E your python interpreter from there. 404s _______________________ ERROR collecting test/test_io.py _______________________ 404s ImportError while importing test module '/tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/test/test_io.py'. 404s Hint: make sure your test modules/packages have valid Python names. 404s Traceback: 404s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 404s return _bootstrap._gcd_import(name[level:], package, level) 404s test/test_io.py:11: in 404s from skgenome import tabio 404s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 404s from . import tabio 404s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 404s import pandas as pd 404s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 404s raise ImportError( 404s E ImportError: Unable to import required dependencies: 404s E numpy: Error importing numpy: you should not try to import numpy from 404s E its source directory; please exit the numpy source tree, and relaunch 404s E your python interpreter from there. 404s _______________________ ERROR collecting test/test_r.py ________________________ 404s ImportError while importing test module '/tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/test/test_r.py'. 404s Hint: make sure your test modules/packages have valid Python names. 404s Traceback: 404s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 404s return _bootstrap._gcd_import(name[level:], package, level) 404s test/test_r.py:14: in 404s import cnvlib 404s /usr/lib/python3/dist-packages/cnvlib/__init__.py:1: in 404s from skgenome.tabio import write 404s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 404s from . import tabio 404s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 404s import pandas as pd 404s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 404s raise ImportError( 404s E ImportError: Unable to import required dependencies: 404s E numpy: Error importing numpy: you should not try to import numpy from 404s E its source directory; please exit the numpy source tree, and relaunch 404s E your python interpreter from there. 404s =========================== short test summary info ============================ 404s ERROR test/test_cnvlib.py 404s ERROR test/test_commands.py 404s ERROR test/test_genome.py 404s ERROR test/test_io.py 404s ERROR test/test_r.py 404s !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! 404s ============================== 5 errors in 0.23s =============================== 404s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build; python3.13 -m pytest test 404s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.oFzITZ/build.sYg/src/data /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build/data; 404s I: pybuild base:311: cd /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build; python3.12 -m pytest test 406s ============================= test session starts ============================== 406s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 406s rootdir: /tmp/autopkgtest.oFzITZ/autopkgtest_tmp/build 406s configfile: pyproject.toml 406s plugins: typeguard-4.4.1 406s collected 64 items 406s 409s test/test_cnvlib.py ......... [ 14%] 425s test/test_commands.py ......................... [ 53%] 428s test/test_genome.py ................... [ 82%] 429s test/test_io.py .......... [ 98%] 437s test/test_r.py . [100%] 437s 437s =============================== warnings summary =============================== 437s test/test_commands.py::CommandTests::test_antitarget 437s test/test_commands.py::CommandTests::test_target 437s test/test_genome.py::GaryTests::test_ranges_resize 437s test/test_io.py::IOTests::test_empty 437s test/test_io.py::IOTests::test_read_auto 437s test/test_io.py::IOTests::test_read_auto 437s test/test_io.py::IOTests::test_read_ilist 437s /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. 437s 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. 437s 437s 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. 437s 437s 437s dframe["gene"].fillna("-", inplace=True) 437s 437s test/test_commands.py: 11 warnings 437s test/test_genome.py: 6 warnings 437s /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. 437s .apply(_merge_overlapping, bp, cmb) 437s 437s test/test_commands.py::CommandTests::test_batch 437s /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. 437s 0. 0. 0. 0. 0. 0. 437s 0. 0. 0. 0. 0. 0. 437s 0. 0. 0. 1.20240481 0.31062124 0.89178357 437s 0. 0. 0. 1.20240481 0.4 0.2004008 437s 0. 0.4008016 0.4 0.4008016 0. 0. 437s 0. 0.4008016 0. 1.20240481 0. 0. 437s 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 437s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 437s 437s test/test_commands.py::CommandTests::test_batch 437s test/test_commands.py::CommandTests::test_batch 437s /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. 437s ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) 437s 437s test/test_commands.py::CommandTests::test_batch 437s test/test_commands.py::CommandTests::test_batch 437s /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. 437s 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 437s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 437s 437s test/test_commands.py: 19 warnings 437s /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. 437s .apply(squash_region) 437s 437s test/test_commands.py: 10 warnings 437s /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)` 437s chrom_col = cnarr["chromosome"].replace( 437s 437s test/test_commands.py::CommandTests::test_coverage 437s test/test_commands.py::CommandTests::test_coverage 437s test/test_commands.py::CommandTests::test_coverage 437s test/test_commands.py::CommandTests::test_coverage 437s /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. 437s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 437s 437s test/test_commands.py::CommandTests::test_export_theta 437s test/test_commands.py::CommandTests::test_export_theta 437s /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)` 437s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 437s 437s test/test_commands.py: 8 warnings 437s test/test_genome.py: 21 warnings 437s /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. 437s table = pd.DataFrame.from_records(rows, columns=columns) 437s 437s test/test_commands.py::CommandTests::test_target 437s test/test_commands.py::CommandTests::test_target 437s test/test_commands.py::CommandTests::test_target 437s test/test_commands.py::CommandTests::test_target 437s test/test_commands.py::CommandTests::test_target 437s test/test_commands.py::CommandTests::test_target 437s test/test_genome.py::GaryTests::test_total_range_size 437s test/test_genome.py::GaryTests::test_total_range_size 437s /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. 437s return sep.join(pd.unique(elems)) 437s 437s test/test_genome.py::GaryTests::test_ranges_resize 437s /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)` 437s limits["upper"] = self.chromosome.replace(chrom_sizes) 437s 437s test/test_genome.py::IntervalTests::test_flatten 437s test/test_genome.py::IntervalTests::test_flatten 437s /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. 437s .apply(_flatten_overlapping, cmb, split_columns) 437s 437s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 437s ====================== 64 passed, 104 warnings in 33.26s ======================= 437s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 437s make: *** [/tmp/PkIrW0sNW9/run:4: pybuild-autopkgtest] Error 25 437s pybuild-autopkgtest: error: /tmp/PkIrW0sNW9/run pybuild-autopkgtest returned exit code 2 438s autopkgtest [08:19:15]: test pybuild-autopkgtest: -----------------------] 439s autopkgtest [08:19:16]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 439s pybuild-autopkgtest FAIL non-zero exit status 25 439s autopkgtest [08:19:16]: @@@@@@@@@@@@@@@@@@@@ summary 439s run-unit-test PASS 439s pybuild-autopkgtest FAIL non-zero exit status 25 612s nova [W] Skipping flock for amd64 612s Creating nova instance adt-plucky-amd64-cnvkit-20241113-081157-juju-7f2275-prod-proposed-migration-environment-20-4aadc13f-6f8c-4de1-b7cf-b80425658c98 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...