0s autopkgtest [11:05:51]: starting date and time: 2024-11-13 11:05:51+0000 0s autopkgtest [11:05:51]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:05:51]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.do94pgnv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-30.secgroup --name adt-plucky-ppc64el-cnvkit-20241113-110551-juju-7f2275-prod-proposed-migration-environment-15-61e2f1fc-a768-4994-aaf8-381a4c9db638 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 116s autopkgtest [11:07:47]: testbed dpkg architecture: ppc64el 116s autopkgtest [11:07:47]: testbed apt version: 2.9.8 116s autopkgtest [11:07:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 117s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 117s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 118s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 118s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [86.2 kB] 118s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [588 kB] 118s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [19.6 kB] 118s Fetched 1715 kB in 1s (1630 kB/s) 118s Reading package lists... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following NEW packages will be installed: 121s python3.13-gdbm 121s The following packages will be upgraded: 121s libpython3-stdlib python3 python3-gdbm python3-minimal 121s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 121s Need to get 102 kB of archives. 121s After this operation, 141 kB of additional disk space will be used. 121s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 122s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 122s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 122s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 122s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 122s Fetched 102 kB in 0s (279 kB/s) 122s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 73767 files and directories currently installed.) 122s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 122s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Setting up python3-minimal (3.12.7-1) ... 123s (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 ... 73767 files and directories currently installed.) 123s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 123s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 123s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 123s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 123s Selecting previously unselected package python3.13-gdbm. 123s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ... 123s Unpacking python3.13-gdbm (3.13.0-2) ... 123s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ... 123s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 123s Setting up python3.13-gdbm (3.13.0-2) ... 123s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 123s Setting up python3 (3.12.7-1) ... 123s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 123s Processing triggers for man-db (2.12.1-3) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 125s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 125s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 125s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 126s Reading package lists... 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [11:08:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 131s autopkgtest [11:08:02]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 136s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (dsc) [2449 B] 136s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (tar) [23.7 MB] 136s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (diff) [17.7 kB] 136s gpgv: Signature made Mon Apr 8 08:42:55 2024 UTC 136s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 136s gpgv: Can't check signature: No public key 136s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found 137s autopkgtest [11:08:08]: testing package cnvkit version 0.9.10-2 138s autopkgtest [11:08:09]: build not needed 145s autopkgtest [11:08:16]: test run-unit-test: preparing testbed 152s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 152s The following additional packages will be installed: 152s blt cnvkit fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 152s fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 libdeflate0 152s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 152s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 152s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 152s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 152s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 152s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 152s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 152s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 152s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 152s python3-cairo python3-contourpy python3-cycler python3-dateutil 152s python3-decorator python3-fonttools python3-freetype python3-fs 152s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 152s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 152s python3-packaging python3-pandas python3-pandas-lib python3-pil 152s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 152s python3-reportlab python3-rlpycairo python3-scipy python3-six 153s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 153s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 153s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 153s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 153s xfonts-encodings xfonts-utils xml-core zip 153s Suggested packages: 153s blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre 153s libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 bwa clustalo clustalw 153s dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons 153s python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools 153s t-coffee wise python-cycler-doc python-joblib-doc python-lxml-doc 153s cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 153s inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi 153s python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado 153s texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 153s python3-gdal python3-pydot python3-pygraphviz gcc gfortran python-numpy-doc 153s python3-dev python3-pytest python-pandas-doc python3-statsmodels 153s python-pil-doc python-pomegranate-doc pdf-viewer python3-egenix-mxtexttools 153s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap 153s python-sklearn-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 153s elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase 153s r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray 153s r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy 153s r-bioc-deseq2 r-bioc-annotate r-cran-runit sgml-base-doc debhelper 153s Recommended packages: 153s javascript-common poppler-data python-biopython-doc ncbi-blast+ 153s python3-pytest python3-simplejson python3-psutil python3-bs4 153s python3-cssselect python3-html5lib python3-bottleneck python3-numexpr 153s python3-odf python3-openpyxl python3-tables python3-olefile 153s fonts-dejavu-extra g++ | c++-compiler isympy-common r-recommended r-base-dev 153s r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 153s x11-utils x11-xserver-utils 153s The following NEW packages will be installed: 153s autopkgtest-satdep blt cnvkit fontconfig fontconfig-config fonts-dejavu-core 153s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 153s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 153s libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 libjbig0 153s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 153s liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 153s libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpoppler140 153s libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 153s libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 153s libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 poppler-utils 153s python-matplotlib-data python3-appdirs python3-biopython python3-brotli 153s python3-cairo python3-contourpy python3-cycler python3-dateutil 153s python3-decorator python3-fonttools python3-freetype python3-fs 153s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 153s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 153s python3-packaging python3-pandas python3-pandas-lib python3-pil 153s python3-pil.imagetk python3-pomegranate python3-pyfaidx python3-pysam 153s python3-reportlab python3-rlpycairo python3-scipy python3-six 153s python3-sklearn python3-sklearn-lib python3-sympy python3-threadpoolctl 153s python3-tk python3-tz python3-ufolib2 python3-unicodedata2 python3.12-tk 153s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 153s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 153s xfonts-encodings xfonts-utils xml-core zip 153s 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 164 MB/164 MB of archives. 153s After this operation, 711 MB of additional disk space will be used. 153s Get:1 /tmp/autopkgtest.Z6Ak3I/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 153s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB] 153s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB] 153s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 153s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 153s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB] 153s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 153s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 153s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB] 153s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB] 154s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB] 154s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB] 154s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 154s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 154s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 154s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB] 154s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB] 154s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B] 154s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 154s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 154s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 154s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB] 155s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB] 155s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-tk ppc64el 3.13.0-2 [107 kB] 155s Get:25 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-tk ppc64el 3.12.7-1 [9752 B] 155s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B] 155s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB] 155s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB] 155s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB] 155s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 155s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB] 155s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB] 155s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 155s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB] 155s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB] 155s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB] 155s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 155s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB] 155s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB] 155s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB] 155s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 155s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB] 155s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB] 155s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB] 155s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 155s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 155s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 155s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 155s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB] 155s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB] 155s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B] 155s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB] 155s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB] 155s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB] 155s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB] 155s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 155s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 155s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB] 155s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3 [2928 kB] 155s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB] 155s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 155s Get:62 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB] 155s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B] 155s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB] 155s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 155s Get:66 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 155s Get:67 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB] 156s Get:68 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB] 156s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB] 156s Get:70 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB] 156s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 156s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB] 156s Get:73 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB] 156s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB] 156s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB] 156s Get:76 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB] 156s Get:77 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build1 [367 kB] 156s Get:78 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB] 156s Get:79 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB] 156s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2 [59.2 kB] 156s Get:81 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 156s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB] 156s Get:83 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3 [4610 kB] 156s Get:84 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB] 156s Get:85 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB] 156s Get:86 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB] 156s Get:87 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 157s Get:88 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pomegranate ppc64el 0.14.8-6 [2700 kB] 157s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-importlib-metadata all 8.5.0-1 [20.7 kB] 157s Get:90 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 157s Get:91 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.1-1 [113 kB] 157s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB] 157s Get:93 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pysam ppc64el 0.22.1+ds-2 [3818 kB] 157s Get:94 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB] 157s Get:95 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB] 157s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 157s Get:97 http://ftpmaster.internal/ubuntu plucky/main ppc64el zip ppc64el 3.0-14ubuntu1 [196 kB] 157s Get:98 http://ftpmaster.internal/ubuntu plucky/main ppc64el unzip ppc64el 6.0-28ubuntu6 [200 kB] 157s Get:99 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper1 ppc64el 1.1.29build1 [13.7 kB] 157s Get:100 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper-utils ppc64el 1.1.29build1 [8742 B] 157s Get:101 http://ftpmaster.internal/ubuntu plucky/main ppc64el xdg-utils all 1.2.1-0ubuntu1 [67.5 kB] 157s Get:102 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-1.1ubuntu2 [192 kB] 157s Get:103 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB] 157s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB] 157s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB] 157s Get:106 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.54.0+ds-3 [272 kB] 157s Get:107 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.54.0+ds-3 [57.5 kB] 157s Get:108 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.54.0+ds-3 [30.6 kB] 157s Get:109 http://ftpmaster.internal/ubuntu plucky/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB] 157s Get:110 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsm6 ppc64el 2:1.2.4-1 [18.4 kB] 157s Get:111 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 157s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-core ppc64el 4.4.2-1 [28.9 MB] 160s Get:113 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-bioc-biocgenerics all 0.50.0-2 [605 kB] 160s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-bioc-dnacopy ppc64el 1.78.0-1 [385 kB] 160s Get:115 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cnvkit all 0.9.10-2 [20.5 MB] 163s Get:116 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpoppler140 ppc64el 24.08.0-1 [1361 kB] 163s Get:117 http://ftpmaster.internal/ubuntu plucky/main ppc64el poppler-utils ppc64el 24.08.0-1 [242 kB] 163s Preconfiguring packages ... 163s Fetched 164 MB in 10s (16.2 MB/s) 163s Selecting previously unselected package sgml-base. 163s (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 ... 73774 files and directories currently installed.) 163s Preparing to unpack .../000-sgml-base_1.31_all.deb ... 163s Unpacking sgml-base (1.31) ... 163s Selecting previously unselected package libtcl8.6:ppc64el. 163s Preparing to unpack .../001-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ... 163s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 163s Selecting previously unselected package fonts-dejavu-mono. 163s Preparing to unpack .../002-fonts-dejavu-mono_2.37-8_all.deb ... 163s Unpacking fonts-dejavu-mono (2.37-8) ... 163s Selecting previously unselected package fonts-dejavu-core. 163s Preparing to unpack .../003-fonts-dejavu-core_2.37-8_all.deb ... 163s Unpacking fonts-dejavu-core (2.37-8) ... 164s Selecting previously unselected package libfontenc1:ppc64el. 164s Preparing to unpack .../004-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ... 164s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ... 164s Selecting previously unselected package x11-common. 164s Preparing to unpack .../005-x11-common_1%3a7.7+23ubuntu3_all.deb ... 164s Unpacking x11-common (1:7.7+23ubuntu3) ... 164s Selecting previously unselected package xfonts-encodings. 164s Preparing to unpack .../006-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 164s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 164s Selecting previously unselected package xfonts-utils. 164s Preparing to unpack .../007-xfonts-utils_1%3a7.7+7_ppc64el.deb ... 164s Unpacking xfonts-utils (1:7.7+7) ... 164s Selecting previously unselected package fonts-urw-base35. 164s Preparing to unpack .../008-fonts-urw-base35_20200910-8_all.deb ... 164s Unpacking fonts-urw-base35 (20200910-8) ... 164s Selecting previously unselected package fontconfig-config. 164s Preparing to unpack .../009-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ... 164s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 164s Selecting previously unselected package libfontconfig1:ppc64el. 164s Preparing to unpack .../010-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ... 164s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 164s Selecting previously unselected package libxrender1:ppc64el. 164s Preparing to unpack .../011-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 164s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 164s Selecting previously unselected package libxft2:ppc64el. 164s Preparing to unpack .../012-libxft2_2.3.6-1build1_ppc64el.deb ... 164s Unpacking libxft2:ppc64el (2.3.6-1build1) ... 164s Selecting previously unselected package libxss1:ppc64el. 164s Preparing to unpack .../013-libxss1_1%3a1.2.3-1build3_ppc64el.deb ... 164s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ... 164s Selecting previously unselected package libtk8.6:ppc64el. 164s Preparing to unpack .../014-libtk8.6_8.6.15-1_ppc64el.deb ... 164s Unpacking libtk8.6:ppc64el (8.6.15-1) ... 164s Selecting previously unselected package tk8.6-blt2.5. 164s Preparing to unpack .../015-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ... 164s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 164s Selecting previously unselected package blt. 164s Preparing to unpack .../016-blt_2.5.3+dfsg-7build1_ppc64el.deb ... 164s Unpacking blt (2.5.3+dfsg-7build1) ... 164s Selecting previously unselected package libblas3:ppc64el. 164s Preparing to unpack .../017-libblas3_3.12.0-3build2_ppc64el.deb ... 164s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 164s Selecting previously unselected package libgfortran5:ppc64el. 164s Preparing to unpack .../018-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 164s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 165s Selecting previously unselected package liblapack3:ppc64el. 165s Preparing to unpack .../019-liblapack3_3.12.0-3build2_ppc64el.deb ... 165s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 165s Selecting previously unselected package python3-numpy. 165s Preparing to unpack .../020-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ... 165s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 165s Selecting previously unselected package python3.12-tk. 165s Preparing to unpack .../021-python3.12-tk_3.12.7-3_ppc64el.deb ... 165s Unpacking python3.12-tk (3.12.7-3) ... 165s Selecting previously unselected package python3.13-tk. 165s Preparing to unpack .../022-python3.13-tk_3.13.0-2_ppc64el.deb ... 165s Unpacking python3.13-tk (3.13.0-2) ... 165s Selecting previously unselected package python3-tk:ppc64el. 165s Preparing to unpack .../023-python3-tk_3.12.7-1_ppc64el.deb ... 165s Unpacking python3-tk:ppc64el (3.12.7-1) ... 165s Selecting previously unselected package python3-pil.imagetk:ppc64el. 165s Preparing to unpack .../024-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ... 165s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 165s Selecting previously unselected package libgomp1:ppc64el. 165s Preparing to unpack .../025-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ... 165s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ... 165s Selecting previously unselected package libimagequant0:ppc64el. 165s Preparing to unpack .../026-libimagequant0_2.18.0-1build1_ppc64el.deb ... 165s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ... 165s Selecting previously unselected package libjpeg-turbo8:ppc64el. 165s Preparing to unpack .../027-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ... 165s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 165s Selecting previously unselected package libjpeg8:ppc64el. 165s Preparing to unpack .../028-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 165s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 165s Selecting previously unselected package liblcms2-2:ppc64el. 165s Preparing to unpack .../029-liblcms2-2_2.16-2_ppc64el.deb ... 165s Unpacking liblcms2-2:ppc64el (2.16-2) ... 165s Selecting previously unselected package libopenjp2-7:ppc64el. 165s Preparing to unpack .../030-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ... 165s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 165s Selecting previously unselected package libgraphite2-3:ppc64el. 165s Preparing to unpack .../031-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 165s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 165s Selecting previously unselected package libharfbuzz0b:ppc64el. 165s Preparing to unpack .../032-libharfbuzz0b_10.0.1-1_ppc64el.deb ... 165s Unpacking libharfbuzz0b:ppc64el (10.0.1-1) ... 165s Selecting previously unselected package libraqm0:ppc64el. 165s Preparing to unpack .../033-libraqm0_0.10.1-1build1_ppc64el.deb ... 165s Unpacking libraqm0:ppc64el (0.10.1-1build1) ... 165s Selecting previously unselected package libdeflate0:ppc64el. 165s Preparing to unpack .../034-libdeflate0_1.22-1_ppc64el.deb ... 165s Unpacking libdeflate0:ppc64el (1.22-1) ... 165s Selecting previously unselected package libjbig0:ppc64el. 165s Preparing to unpack .../035-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ... 165s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ... 165s Selecting previously unselected package liblerc4:ppc64el. 165s Preparing to unpack .../036-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ... 165s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ... 165s Selecting previously unselected package libsharpyuv0:ppc64el. 165s Preparing to unpack .../037-libsharpyuv0_1.4.0-0.1_ppc64el.deb ... 165s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ... 165s Selecting previously unselected package libwebp7:ppc64el. 165s Preparing to unpack .../038-libwebp7_1.4.0-0.1_ppc64el.deb ... 165s Unpacking libwebp7:ppc64el (1.4.0-0.1) ... 165s Selecting previously unselected package libtiff6:ppc64el. 165s Preparing to unpack .../039-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ... 165s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 165s Selecting previously unselected package libwebpdemux2:ppc64el. 165s Preparing to unpack .../040-libwebpdemux2_1.4.0-0.1_ppc64el.deb ... 165s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ... 165s Selecting previously unselected package libwebpmux3:ppc64el. 165s Preparing to unpack .../041-libwebpmux3_1.4.0-0.1_ppc64el.deb ... 165s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ... 165s Selecting previously unselected package python3-pil:ppc64el. 165s Preparing to unpack .../042-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ... 165s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ... 165s Selecting previously unselected package libpixman-1-0:ppc64el. 165s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_ppc64el.deb ... 165s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 166s Selecting previously unselected package libxcb-render0:ppc64el. 166s Preparing to unpack .../044-libxcb-render0_1.17.0-2_ppc64el.deb ... 166s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 166s Selecting previously unselected package libxcb-shm0:ppc64el. 166s Preparing to unpack .../045-libxcb-shm0_1.17.0-2_ppc64el.deb ... 166s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 166s Selecting previously unselected package libcairo2:ppc64el. 166s Preparing to unpack .../046-libcairo2_1.18.2-2_ppc64el.deb ... 166s Unpacking libcairo2:ppc64el (1.18.2-2) ... 166s Selecting previously unselected package python3-cairo. 166s Preparing to unpack .../047-python3-cairo_1.26.1-2_ppc64el.deb ... 166s Unpacking python3-cairo (1.26.1-2) ... 166s Selecting previously unselected package python3-freetype. 166s Preparing to unpack .../048-python3-freetype_2.5.1-1_all.deb ... 166s Unpacking python3-freetype (2.5.1-1) ... 166s Selecting previously unselected package python3-rlpycairo. 166s Preparing to unpack .../049-python3-rlpycairo_0.3.0-3_all.deb ... 166s Unpacking python3-rlpycairo (0.3.0-3) ... 166s Selecting previously unselected package python3-reportlab. 166s Preparing to unpack .../050-python3-reportlab_4.2.5-1_all.deb ... 166s Unpacking python3-reportlab (4.2.5-1) ... 166s Selecting previously unselected package xml-core. 166s Preparing to unpack .../051-xml-core_0.19_all.deb ... 166s Unpacking xml-core (0.19) ... 166s Selecting previously unselected package w3c-sgml-lib. 166s Preparing to unpack .../052-w3c-sgml-lib_1.3-3_all.deb ... 166s Unpacking w3c-sgml-lib (1.3-3) ... 166s Selecting previously unselected package python3-biopython. 166s Preparing to unpack .../053-python3-biopython_1.84+dfsg-4_ppc64el.deb ... 166s Unpacking python3-biopython (1.84+dfsg-4) ... 166s Selecting previously unselected package libjs-jquery. 166s Preparing to unpack .../054-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 166s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 166s Selecting previously unselected package libjs-jquery-ui. 166s Preparing to unpack .../055-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 166s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 166s Selecting previously unselected package fonts-lyx. 166s Preparing to unpack .../056-fonts-lyx_2.4.2.1-1_all.deb ... 166s Unpacking fonts-lyx (2.4.2.1-1) ... 166s Selecting previously unselected package python-matplotlib-data. 166s Preparing to unpack .../057-python-matplotlib-data_3.8.3-3_all.deb ... 166s Unpacking python-matplotlib-data (3.8.3-3) ... 166s Selecting previously unselected package python3-six. 166s Preparing to unpack .../058-python3-six_1.16.0-7_all.deb ... 166s Unpacking python3-six (1.16.0-7) ... 166s Selecting previously unselected package python3-dateutil. 166s Preparing to unpack .../059-python3-dateutil_2.9.0-2_all.deb ... 166s Unpacking python3-dateutil (2.9.0-2) ... 166s Selecting previously unselected package python3-contourpy. 166s Preparing to unpack .../060-python3-contourpy_1.3.0-2_ppc64el.deb ... 166s Unpacking python3-contourpy (1.3.0-2) ... 166s Selecting previously unselected package python3-cycler. 166s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 166s Unpacking python3-cycler (0.12.1-1) ... 166s Selecting previously unselected package python3-brotli. 166s Preparing to unpack .../062-python3-brotli_1.1.0-2build2_ppc64el.deb ... 166s Unpacking python3-brotli (1.1.0-2build2) ... 166s Selecting previously unselected package python3-decorator. 166s Preparing to unpack .../063-python3-decorator_5.1.1-5_all.deb ... 166s Unpacking python3-decorator (5.1.1-5) ... 166s Selecting previously unselected package liblbfgsb0:ppc64el. 166s Preparing to unpack .../064-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 166s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 166s Selecting previously unselected package python3-scipy. 166s Preparing to unpack .../065-python3-scipy_1.13.1-5_ppc64el.deb ... 166s Unpacking python3-scipy (1.13.1-5) ... 167s Selecting previously unselected package python3-ufolib2. 167s Preparing to unpack .../066-python3-ufolib2_0.16.1+dfsg1-1_all.deb ... 167s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ... 167s Selecting previously unselected package python3-mpmath. 167s Preparing to unpack .../067-python3-mpmath_1.3.0-1_all.deb ... 167s Unpacking python3-mpmath (1.3.0-1) ... 167s Selecting previously unselected package python3-sympy. 167s Preparing to unpack .../068-python3-sympy_1.13.3-1_all.deb ... 167s Unpacking python3-sympy (1.13.3-1) ... 167s Selecting previously unselected package python3-tz. 167s Preparing to unpack .../069-python3-tz_2024.1-2_all.deb ... 167s Unpacking python3-tz (2024.1-2) ... 167s Selecting previously unselected package python3-appdirs. 167s Preparing to unpack .../070-python3-appdirs_1.4.4-4_all.deb ... 167s Unpacking python3-appdirs (1.4.4-4) ... 167s Selecting previously unselected package python3-fs. 167s Preparing to unpack .../071-python3-fs_2.4.16-4_all.deb ... 167s Unpacking python3-fs (2.4.16-4) ... 168s Selecting previously unselected package libxslt1.1:ppc64el. 168s Preparing to unpack .../072-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ... 168s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 168s Selecting previously unselected package python3-lxml:ppc64el. 168s Preparing to unpack .../073-python3-lxml_5.3.0-1_ppc64el.deb ... 168s Unpacking python3-lxml:ppc64el (5.3.0-1) ... 168s Selecting previously unselected package python3-lz4. 168s Preparing to unpack .../074-python3-lz4_4.0.2+dfsg-1build4_ppc64el.deb ... 168s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 168s Selecting previously unselected package python3-unicodedata2. 168s Preparing to unpack .../075-python3-unicodedata2_15.1.0+ds-1build1_ppc64el.deb ... 168s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 168s Selecting previously unselected package unicode-data. 168s Preparing to unpack .../076-unicode-data_15.1.0-1_all.deb 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(3.8.3-3) ... 168s Selecting previously unselected package python3-pandas-lib:ppc64el. 168s Preparing to unpack .../082-python3-pandas-lib_2.2.3+dfsg-5_ppc64el.deb ... 168s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ... 168s Selecting previously unselected package python3-pandas. 168s Preparing to unpack .../083-python3-pandas_2.2.3+dfsg-5_all.deb ... 168s Unpacking python3-pandas (2.2.3+dfsg-5) ... 169s Selecting previously unselected package python3-joblib. 169s Preparing to unpack .../084-python3-joblib_1.3.2-5_all.deb ... 169s Unpacking python3-joblib (1.3.2-5) ... 169s Selecting previously unselected package python3-networkx. 169s Preparing to unpack .../085-python3-networkx_3.2.1-4ubuntu1_all.deb ... 169s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 169s Selecting previously unselected package python3-pomegranate. 169s Preparing to unpack .../086-python3-pomegranate_0.14.8-6_ppc64el.deb ... 169s Unpacking python3-pomegranate (0.14.8-6) ... 170s Selecting previously unselected package python3-importlib-metadata. 170s Preparing to unpack .../087-python3-importlib-metadata_8.5.0-1_all.deb ... 170s Unpacking python3-importlib-metadata (8.5.0-1) ... 170s Selecting previously unselected package python3-pyfaidx. 170s Preparing to unpack .../088-python3-pyfaidx_0.8.1.3-1_all.deb ... 170s Unpacking python3-pyfaidx (0.8.1.3-1) ... 170s Selecting previously unselected package libhtscodecs2:ppc64el. 170s Preparing to unpack .../089-libhtscodecs2_1.6.1-1_ppc64el.deb ... 170s Unpacking libhtscodecs2:ppc64el (1.6.1-1) ... 170s Selecting previously unselected package libhts3t64:ppc64el. 170s Preparing to unpack .../090-libhts3t64_1.20+ds-1_ppc64el.deb ... 170s Unpacking libhts3t64:ppc64el (1.20+ds-1) ... 170s Selecting previously unselected package python3-pysam. 170s Preparing to unpack .../091-python3-pysam_0.22.1+ds-2_ppc64el.deb ... 170s Unpacking python3-pysam (0.22.1+ds-2) ... 170s Selecting previously unselected package python3-threadpoolctl. 170s Preparing to unpack .../092-python3-threadpoolctl_3.1.0-1_all.deb ... 170s Unpacking python3-threadpoolctl (3.1.0-1) ... 170s Selecting previously unselected package python3-sklearn-lib:ppc64el. 170s Preparing to unpack .../093-python3-sklearn-lib_1.4.2+dfsg-6_ppc64el.deb ... 170s Unpacking python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 170s Selecting previously unselected package python3-sklearn. 170s Preparing to unpack .../094-python3-sklearn_1.4.2+dfsg-6_all.deb ... 170s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 170s Selecting previously unselected package zip. 170s Preparing to unpack .../095-zip_3.0-14ubuntu1_ppc64el.deb ... 170s Unpacking zip (3.0-14ubuntu1) ... 170s Selecting previously unselected package unzip. 170s Preparing to unpack .../096-unzip_6.0-28ubuntu6_ppc64el.deb ... 170s Unpacking unzip (6.0-28ubuntu6) ... 171s Selecting previously unselected package libpaper1:ppc64el. 171s Preparing to unpack .../097-libpaper1_1.1.29build1_ppc64el.deb ... 171s Unpacking libpaper1:ppc64el (1.1.29build1) ... 171s Selecting previously unselected package libpaper-utils. 171s Preparing to unpack .../098-libpaper-utils_1.1.29build1_ppc64el.deb ... 171s Unpacking libpaper-utils (1.1.29build1) ... 171s Selecting previously unselected package xdg-utils. 171s Preparing to unpack .../099-xdg-utils_1.2.1-0ubuntu1_all.deb ... 171s Unpacking xdg-utils (1.2.1-0ubuntu1) ... 171s Selecting previously unselected package fontconfig. 171s Preparing to unpack .../100-fontconfig_2.15.0-1.1ubuntu2_ppc64el.deb ... 171s Unpacking fontconfig (2.15.0-1.1ubuntu2) ... 171s Selecting previously unselected package libthai-data. 171s Preparing to unpack .../101-libthai-data_0.1.29-2build1_all.deb ... 171s Unpacking libthai-data (0.1.29-2build1) ... 171s Selecting previously unselected package libdatrie1:ppc64el. 171s Preparing to unpack .../102-libdatrie1_0.2.13-3build1_ppc64el.deb ... 171s Unpacking libdatrie1:ppc64el (0.2.13-3build1) ... 171s Selecting previously unselected package libthai0:ppc64el. 171s Preparing to unpack .../103-libthai0_0.1.29-2build1_ppc64el.deb ... 171s Unpacking libthai0:ppc64el (0.1.29-2build1) ... 171s Selecting previously unselected package libpango-1.0-0:ppc64el. 171s Preparing to unpack .../104-libpango-1.0-0_1.54.0+ds-3_ppc64el.deb ... 171s Unpacking libpango-1.0-0:ppc64el (1.54.0+ds-3) ... 171s Selecting previously unselected package libpangoft2-1.0-0:ppc64el. 171s Preparing to unpack .../105-libpangoft2-1.0-0_1.54.0+ds-3_ppc64el.deb ... 171s Unpacking libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ... 171s Selecting previously unselected package libpangocairo-1.0-0:ppc64el. 171s Preparing to unpack .../106-libpangocairo-1.0-0_1.54.0+ds-3_ppc64el.deb ... 171s Unpacking libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ... 171s Selecting previously unselected package libice6:ppc64el. 171s Preparing to unpack .../107-libice6_2%3a1.1.1-1_ppc64el.deb ... 171s Unpacking libice6:ppc64el (2:1.1.1-1) ... 171s Selecting previously unselected package libsm6:ppc64el. 171s Preparing to unpack .../108-libsm6_2%3a1.2.4-1_ppc64el.deb ... 171s Unpacking libsm6:ppc64el (2:1.2.4-1) ... 171s Selecting previously unselected package libxt6t64:ppc64el. 171s Preparing to unpack .../109-libxt6t64_1%3a1.2.1-1.2build1_ppc64el.deb ... 171s Unpacking libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 171s Selecting previously unselected package r-base-core. 171s Preparing to unpack .../110-r-base-core_4.4.2-1_ppc64el.deb ... 171s Unpacking r-base-core (4.4.2-1) ... 171s Selecting previously unselected package r-bioc-biocgenerics. 171s Preparing to unpack .../111-r-bioc-biocgenerics_0.50.0-2_all.deb ... 171s Unpacking r-bioc-biocgenerics (0.50.0-2) ... 171s Selecting previously unselected package r-bioc-dnacopy. 171s Preparing to unpack .../112-r-bioc-dnacopy_1.78.0-1_ppc64el.deb ... 171s Unpacking r-bioc-dnacopy (1.78.0-1) ... 171s Selecting previously unselected package cnvkit. 171s Preparing to unpack .../113-cnvkit_0.9.10-2_all.deb ... 171s Unpacking cnvkit (0.9.10-2) ... 172s Selecting previously unselected package libpoppler140:ppc64el. 172s Preparing to unpack .../114-libpoppler140_24.08.0-1_ppc64el.deb ... 172s Unpacking libpoppler140:ppc64el (24.08.0-1) ... 172s Selecting previously unselected package poppler-utils. 172s Preparing to unpack .../115-poppler-utils_24.08.0-1_ppc64el.deb ... 172s Unpacking poppler-utils (24.08.0-1) ... 172s Selecting previously unselected package autopkgtest-satdep. 172s Preparing to unpack .../116-1-autopkgtest-satdep.deb ... 172s Unpacking autopkgtest-satdep (0) ... 172s Setting up libhtscodecs2:ppc64el (1.6.1-1) ... 172s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 172s Setting up liblcms2-2:ppc64el (2.16-2) ... 172s Setting up libpixman-1-0:ppc64el (0.44.0-3) ... 172s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ... 172s Setting up libpaper1:ppc64el (1.1.29build1) ... 172s 172s Creating config file /etc/papersize with new version 172s Setting up liblerc4:ppc64el 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(2.1-6.1ubuntu2) ... 175s Setting up python3-tz (2024.1-2) ... 175s Setting up unicode-data (15.1.0-1) ... 175s Setting up python3-six (1.16.0-7) ... 175s Setting up python3-decorator (5.1.1-5) ... 176s Setting up zip (3.0-14ubuntu1) ... 176s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ... 176s Setting up libblas3:ppc64el (3.12.0-3build2) ... 176s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 176s Setting up python3-packaging (24.1-1) ... 176s Setting up python3-brotli (1.1.0-2build2) ... 176s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 176s Setting up python3-cycler (0.12.1-1) ... 176s Setting up libimagequant0:ppc64el (2.18.0-1build1) ... 176s Setting up fonts-dejavu-mono (2.37-8) ... 176s Setting up python3-kiwisolver (1.4.7-2) ... 176s Setting up libtcl8.6:ppc64el (8.6.15+dfsg-2) ... 176s Setting up fonts-dejavu-core (2.37-8) ... 176s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ... 176s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 176s Setting up libwebp7:ppc64el (1.4.0-0.1) ... 176s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ... 176s Setting up libhts3t64:ppc64el (1.20+ds-1) ... 176s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ... 176s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ... 176s Setting up libthai-data (0.1.29-2build1) ... 176s Setting up python3-dateutil (2.9.0-2) ... 176s Setting up sgml-base (1.31) ... 176s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 176s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 176s Setting up python3-mpmath (1.3.0-1) ... 177s Setting up python-matplotlib-data (3.8.3-3) ... 177s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ... 177s Setting up python3-appdirs (1.4.4-4) ... 177s Setting up xdg-utils (1.2.1-0ubuntu1) ... 177s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 177s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 177s Setting up python3-pyfaidx (0.8.1.3-1) ... 177s Setting up python3-sympy (1.13.3-1) ... 185s Setting up libice6:ppc64el (2:1.1.1-1) ... 185s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 185s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 185s Setting up python3-pysam (0.22.1+ds-2) ... 185s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 185s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ... 185s Setting up xfonts-utils (1:7.7+7) ... 185s Setting up python3-fs (2.4.16-4) ... 186s Setting up libthai0:ppc64el (0.1.29-2build1) ... 186s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 186s Setting up libraqm0:ppc64el (0.10.1-1build1) ... 186s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 188s Setting up python3-lxml:ppc64el (5.3.0-1) ... 188s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 188s Setting up xml-core (0.19) ... 188s Setting up python3-contourpy (1.3.0-2) ... 189s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ... 189s Setting up libsm6:ppc64el (2:1.2.4-1) ... 189s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 189s Setting up fontconfig (2.15.0-1.1ubuntu2) ... 191s Regenerating fonts cache... done. 191s Setting up libxft2:ppc64el (2.3.6-1build1) ... 191s Setting up python3-scipy (1.13.1-5) ... 195s Setting up python3-pomegranate (0.14.8-6) ... 195s Setting up libtk8.6:ppc64el (8.6.15-1) ... 195s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ... 195s Setting up libpango-1.0-0:ppc64el (1.54.0+ds-3) ... 195s Setting up python3.12-tk (3.12.7-3) ... 195s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ... 195s Setting up fonts-urw-base35 (20200910-8) ... 196s Setting up libcairo2:ppc64el (1.18.2-2) ... 196s Setting up python3.13-tk (3.13.0-2) ... 196s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ... 196s Setting up python3-pandas (2.2.3+dfsg-5) ... 203s Setting up libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 203s Setting up python3-sklearn (1.4.2+dfsg-6) ... 205s Setting up libpoppler140:ppc64el (24.08.0-1) ... 205s Setting up poppler-utils (24.08.0-1) ... 205s Setting up libpangoft2-1.0-0:ppc64el (1.54.0+ds-3) ... 205s Setting up libpangocairo-1.0-0:ppc64el (1.54.0+ds-3) ... 205s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 205s Setting up python3-cairo (1.26.1-2) ... 205s Setting up blt (2.5.3+dfsg-7build1) ... 205s Setting up python3-tk:ppc64el (3.12.7-1) ... 205s Setting up python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ... 205s Setting up python3-rlpycairo (0.3.0-3) ... 205s Setting up r-base-core (4.4.2-1) ... 206s 206s Creating config file /etc/R/Renviron with new version 206s Setting up python3-reportlab (4.2.5-1) ... 207s Setting up r-bioc-biocgenerics (0.50.0-2) ... 207s Setting up r-bioc-dnacopy (1.78.0-1) ... 207s Setting up python3-fonttools (4.46.0-1build2) ... 208s Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... 208s Setting up python3-matplotlib (3.8.3-3) ... 210s Processing triggers for libc-bin (2.40-1ubuntu3) ... 210s Processing triggers for man-db (2.12.1-3) ... 212s Processing triggers for install-info (7.1.1-1) ... 212s Processing triggers for sgml-base (1.31) ... 212s Setting up w3c-sgml-lib (1.3-3) ... 249s Setting up python3-biopython (1.84+dfsg-4) ... 250s Setting up cnvkit (0.9.10-2) ... 251s Setting up autopkgtest-satdep (0) ... 258s (Reading database ... 90993 files and directories currently installed.) 258s Removing autopkgtest-satdep (0) ... 261s autopkgtest [11:10:12]: test run-unit-test: [----------------------- 261s 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/ 264s Created directory build/ 265s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 265s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 265s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 265s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 265s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 265s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 265s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 265s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 265s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 265s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 267s Number of target and antitarget files: 3, 3 267s No FASTA reference genome provided; skipping GC, RM calculations 267s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 267s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 267s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 267s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 267s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 267s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 267s Loading build/p2-20_5.targetcoverage.cnn 268s Correcting for GC bias... 268s Correcting for density bias... 268s Loading build/p2-5_5.targetcoverage.cnn 268s Correcting for GC bias... 268s Correcting for density bias... 268s Loading build/p2-9_5.targetcoverage.cnn 268s Correcting for GC bias... 268s Correcting for density bias... 268s Loading build/p2-20_5.antitargetcoverage.cnn 268s Correcting for GC bias... 268s Loading build/p2-5_5.antitargetcoverage.cnn 268s Correcting for GC bias... 268s Loading build/p2-9_5.antitargetcoverage.cnn 268s Correcting for GC bias... 268s Calculating average bin coverages 280s Calculating bin spreads 282s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 282s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 282s " chr1:2435319-2436685 log2=-0.709 spread=0.503 282s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 282s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 282s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 282s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 282s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 282s " chr1:120611883-120612051 log2=0.070 spread=0.050 282s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 282s " chr1:156842391-156842479 log2=-0.398 spread=0.290 282s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 282s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 282s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 282s " chr1:183481886-183481951 log2=-0.040 spread=0.119 282s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 282s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 282s " chr1:243800859-243801066 log2=0.023 spread=0.063 282s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 282s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 282s " chr2:25536716-25536891 log2=0.702 spread=0.033 282s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 282s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 282s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 282s REL chr2:61108881-61109061 log2=1.026 spread=0.559 282s " chr2:61128072-61128256 log2=0.115 spread=0.173 282s " chr2:61145275-61145462 log2=0.014 spread=0.099 282s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 282s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 282s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 282s " chr2:128095237-128095425 log2=0.215 spread=0.212 282s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 282s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 282s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 282s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 282s " chr3:97160189-97160367 log2=-0.050 spread=0.191 282s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 282s " chr3:142286854-142287031 log2=-0.076 spread=0.116 282s GAK chr4:896278-896357 log2=-1.505 spread=1.261 282s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 282s " chr4:1803044-1803507 log2=-0.073 spread=0.117 282s " chr4:1808792-1809022 log2=0.252 spread=0.108 282s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 282s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 282s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 282s " chr4:178514600-178514725 log2=-0.098 spread=0.096 282s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 282s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 282s " chr5:1295312-1295381 log2=-0.690 spread=0.462 282s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 282s " chr5:25519857-25520034 log2=-0.015 spread=0.095 282s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 282s " chr5:38962338-38962525 log2=0.005 spread=0.019 282s " chr5:38966685-38966862 log2=0.006 spread=0.165 282s " chr5:38978620-38978763 log2=0.040 spread=0.030 282s " chr5:39074133-39074327 log2=-0.158 spread=0.139 282s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 282s " chr5:51030131-51030313 log2=-0.034 spread=0.192 282s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 282s " chr5:56168412-56168590 log2=0.479 spread=0.038 282s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 282s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 282s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 282s " chr5:86637023-86637168 log2=0.054 spread=0.111 282s " chr5:86642414-86642592 log2=0.254 spread=0.162 282s " chr5:86648912-86649096 log2=0.092 spread=0.062 282s " chr5:86670598-86670778 log2=0.222 spread=0.198 282s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 282s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 282s APC chr5:112101965-112102138 log2=0.104 spread=0.217 282s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 282s " chr5:170837567-170837631 log2=0.085 spread=0.349 282s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 282s " chr5:180046203-180046404 log2=-1.531 spread=0.722 282s " chr5:180076418-180076603 log2=-2.224 spread=1.416 282s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 282s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 282s " chr6:31939599-31940313 log2=-19.582 spread=0.181 282s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 282s " chr6:31946632-31946824 log2=-20.052 spread=0.088 282s " chr6:31947142-31947366 log2=-20.114 spread=0.066 282s " chr6:31948176-31948360 log2=-19.982 spread=0.149 282s " chr6:31948382-31948612 log2=-19.757 spread=0.165 282s " chr6:31948730-31949253 log2=-20.048 spread=0.014 282s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 282s " chr6:32164046-32164227 log2=-19.755 spread=0.189 282s " chr6:32164652-32164888 log2=-19.984 spread=0.154 282s " chr6:32165021-32165403 log2=-19.625 spread=0.196 282s " chr6:32166163-32166545 log2=-20.043 spread=0.072 282s " chr6:32166648-32166962 log2=-3.514 spread=5.742 282s " chr6:32168554-32168821 log2=-19.601 spread=0.197 282s " chr6:32168844-32169306 log2=-19.683 spread=0.166 282s " chr6:32169801-32170391 log2=-19.405 spread=0.205 282s " chr6:32171492-32171691 log2=-20.095 spread=0.101 282s " chr6:32171861-32172198 log2=-3.141 spread=7.288 282s " chr6:32178478-32178749 log2=-19.927 spread=0.164 282s " chr6:32180197-32180441 log2=-10.902 spread=9.532 282s " chr6:32180544-32180722 log2=-19.675 spread=0.186 282s " chr6:32180857-32181062 log2=-19.562 spread=0.227 282s " chr6:32181411-32181646 log2=-19.966 spread=0.171 282s " chr6:32181832-32182066 log2=-19.961 spread=0.172 282s " chr6:32182948-32183194 log2=-19.935 spread=0.168 282s " chr6:32184667-32185079 log2=-19.923 spread=0.165 282s " chr6:32185720-32185919 log2=-19.707 spread=0.197 282s " chr6:32187317-32187601 log2=-19.765 spread=0.173 282s " chr6:32187871-32188094 log2=-19.660 spread=0.188 282s " chr6:32188127-32188451 log2=-19.622 spread=0.169 282s " chr6:32188481-32188693 log2=-19.902 spread=0.132 282s " chr6:32188704-32189133 log2=-19.501 spread=0.193 282s " chr6:32190258-32190616 log2=-19.570 spread=0.209 282s " chr6:32190724-32190908 log2=-19.540 spread=0.232 282s " chr6:32191570-32191668 log2=-19.773 spread=0.178 282s " chr6:32191676-32191753 log2=-19.374 spread=0.201 282s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 282s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 282s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 282s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 282s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 282s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 282s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 282s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 282s " chr6:128316545-128316699 log2=-0.070 spread=0.050 282s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 282s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 282s " chr6:157099442-157099991 log2=-0.846 spread=0.504 282s " chr6:157100042-157100634 log2=-1.570 spread=0.825 282s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 282s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 282s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 282s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 282s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 282s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 282s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 282s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 282s " chr7:98491365-98491541 log2=0.209 spread=0.153 282s " chr7:98493314-98493496 log2=0.389 spread=0.207 282s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 282s " chr7:128829048-128829358 log2=-0.474 spread=0.315 282s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 282s " chr7:140484736-140484912 log2=0.081 spread=0.150 282s " chr7:140487956-140488430 log2=-0.089 spread=0.142 282s " chr7:140493336-140493442 log2=-0.340 spread=0.283 282s " chr7:140624315-140624540 log2=-0.497 spread=0.342 282s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 282s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 282s " chr8:30941153-30941335 log2=0.079 spread=0.294 282s " chr8:30942625-30942802 log2=0.044 spread=0.247 282s " chr8:30947918-30948092 log2=0.151 spread=0.124 282s " chr8:31000128-31000252 log2=-0.099 spread=0.098 282s " chr8:31001006-31001182 log2=-0.002 spread=0.062 282s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 282s " chr8:37698557-37699898 log2=-0.612 spread=0.029 282s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 282s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 282s " chr8:48845528-48845758 log2=0.056 spread=0.196 282s " chr8:48866846-48867043 log2=-0.067 spread=0.097 282s " chr8:48868369-48868526 log2=-0.239 spread=0.174 282s " chr8:48872485-48872722 log2=-0.636 spread=0.464 282s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 282s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 282s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 282s " chr9:2101491-2101640 log2=0.244 spread=0.104 282s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 282s " chr9:5067014-5067883 log2=0.146 spread=0.089 282s " chr9:5068184-5070306 log2=0.133 spread=0.092 282s " chr9:5076944-5077152 log2=0.046 spread=0.137 282s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 282s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 282s " chr9:21986759-21986899 log2=0.058 spread=0.175 282s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 282s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 282s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 282s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 282s " chr9:87425375-87425452 log2=0.494 spread=0.066 282s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 282s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 282s " chr9:139250747-139251032 log2=-0.223 spread=0.273 282s " chr9:139252418-139252703 log2=-0.512 spread=0.264 282s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 282s " chr9:139417262-139417677 log2=-0.173 spread=0.191 282s " chr9:139440110-139440287 log2=-1.257 spread=0.500 282s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 282s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 282s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 282s " chr10:43600360-43600677 log2=-0.341 spread=0.222 282s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 282s " chr10:89685254-89685374 log2=0.244 spread=0.259 282s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 282s " chr10:93579008-93579121 log2=0.166 spread=0.220 282s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 282s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 282s " chr10:112679716-112679934 log2=-0.008 spread=0.028 282s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 282s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 282s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 282s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 282s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 282s " chr11:94170270-94170454 log2=0.095 spread=0.285 282s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 282s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 282s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 282s " chr11:108164020-108164234 log2=-0.056 spread=0.040 282s " chr11:108217986-108218135 log2=0.359 spread=0.277 282s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 282s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 282s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 282s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 282s " chr12:25391004-25391186 log2=0.368 spread=0.128 282s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 282s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 282s " chr12:51206782-51207287 log2=-0.012 spread=0.101 282s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 282s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 282s " chr13:26970356-26970536 log2=0.137 spread=0.121 282s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 282s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 282s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 282s " chr13:32903506-32903689 log2=0.019 spread=0.232 282s " chr13:32918645-32918823 log2=0.158 spread=0.114 282s " chr13:32920899-32921077 log2=0.014 spread=0.247 282s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 282s " chr13:48919164-48919369 log2=0.025 spread=0.094 282s " chr13:48921877-48922044 log2=0.106 spread=0.147 282s " chr13:48923026-48923204 log2=0.360 spread=0.016 282s " chr13:48938965-48939147 log2=0.084 spread=0.356 282s " chr13:48941578-48941767 log2=0.238 spread=0.212 282s " chr13:48947486-48947665 log2=0.025 spread=0.126 282s " chr13:48954166-48954251 log2=0.061 spread=0.273 282s " chr13:49037815-49038005 log2=0.063 spread=0.062 282s " chr13:49047410-49047589 log2=0.053 spread=0.170 282s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 282s " chr13:85527771-85527948 log2=0.007 spread=0.222 282s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 282s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 282s " chr13:110438332-110438432 log2=-3.643 spread=2.325 282s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 282s " chr14:20291466-20291612 log2=0.697 spread=0.248 282s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 282s " chr14:36989195-36989373 log2=0.023 spread=0.162 282s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 282s " chr14:50619741-50619923 log2=0.003 spread=0.272 282s " chr14:50697856-50698044 log2=0.277 spread=0.334 282s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 282s " chr14:71275790-71275923 log2=-2.815 spread=1.938 282s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 282s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 282s " chr15:38544477-38545455 log2=-0.348 spread=0.179 282s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 282s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 282s " chr15:41803968-41804185 log2=-2.202 spread=0.188 282s " chr15:41804261-41804494 log2=-0.402 spread=0.392 282s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 282s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 282s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 282s " chr16:2611404-2611585 log2=-5.171 spread=1.963 282s " chr16:2611721-2611943 log2=-11.810 spread=9.172 282s " chr16:2615504-2615725 log2=-20.113 spread=0.007 282s " chr16:2616307-2616486 log2=-20.054 spread=0.072 282s " chr16:2631267-2631414 log2=-20.009 spread=0.061 282s " chr16:2631583-2631734 log2=-20.089 spread=0.090 282s " chr16:2633363-2633616 log2=-20.101 spread=0.089 282s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 282s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 282s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 282s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 282s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 282s " chr16:50826460-50826650 log2=0.239 spread=0.204 282s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 282s " chr16:60005694-60005857 log2=-0.366 spread=0.298 282s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 282s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 282s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 282s " chr17:12011053-12011253 log2=0.028 spread=0.232 282s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 282s " chr17:29496854-29497046 log2=0.226 spread=0.193 282s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 282s " chr17:30519172-30519355 log2=0.163 spread=0.289 282s " chr17:30525911-30526093 log2=-0.157 spread=0.046 282s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 282s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 282s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 282s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 282s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 282s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 282s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 282s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 282s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 282s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 282s " chr19:2210351-2210545 log2=-0.860 spread=0.261 282s " chr19:2226130-2227152 log2=-0.113 spread=0.120 282s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 282s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 282s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 282s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 282s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 282s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 282s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 282s " chr19:15311544-15311749 log2=-1.887 spread=1.202 282s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 282s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 282s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 282s " chr19:33792774-33793010 log2=-1.781 spread=0.127 282s " chr19:33793014-33793356 log2=-0.541 spread=0.385 282s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 282s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 282s " chr19:45873698-45873881 log2=-0.522 spread=0.327 282s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 282s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 282s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 282s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 282s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 282s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 282s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 282s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 282s " chr21:36265140-36265318 log2=0.042 spread=0.039 282s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 282s " chr22:29115325-29115465 log2=0.055 spread=0.390 282s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 282s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 282s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 282s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 282s " chrX:1317372-1317594 log2=-21.121 spread=0.049 282s " chrX:1321225-1321435 log2=-20.851 spread=0.196 282s " chrX:1325274-1325530 log2=-21.121 spread=0.011 282s " chrX:1327651-1327830 log2=-21.000 spread=0.029 282s " chrX:1331391-1331576 log2=-21.018 spread=0.052 282s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 282s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 282s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 282s " chrX:123185143-123185290 log2=-1.018 spread=0.062 282s " chrX:123202378-123202544 log2=-0.959 spread=0.103 282s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 282s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 282s " chrY:9008607-9008759 log2=-1.012 spread=0.097 282s " chrY:13131970-13132039 log2=-1.004 spread=0.074 282s " chrY:19506485-19506650 log2=-1.018 spread=0.034 282s " chrY:21033918-21034071 log2=-1.013 spread=0.057 282s " chrY:28463435-28463622 log2=-0.952 spread=0.039 282s " chrY:28514033-28514208 log2=-0.992 spread=0.026 282s Antitargets: 108 (0.8597%) bins failed filters 282s Wrote build/reference-picard.cnn with 19209 regions 283s 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 285s Processing target: p2-5_5 285s Keeping 6308 of 6646 bins 285s Correcting for GC bias... 285s Correcting for density bias... 285s Processing antitarget: p2-5_5 285s Keeping 12455 of 12563 bins 285s Correcting for GC bias... 285s WARNING: Skipping correction for RepeatMasker bias 285s Targets are 1.18 x more variable than antitargets 285s Wrote build/p2-5_5.cnr with 18763 regions 286s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 287s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 287s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 288s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 291s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 291s 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 292s Processing target: p2-9_2 292s Keeping 6308 of 6646 bins 292s Correcting for GC bias... 292s Correcting for density bias... 292s Processing antitarget: p2-9_2 292s Keeping 12455 of 12563 bins 292s Correcting for GC bias... 292s WARNING: Skipping correction for RepeatMasker bias 292s Targets are 1.72 x more variable than antitargets 293s Wrote build/p2-9_2.cnr with 18763 regions 293s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 294s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 295s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 295s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 297s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 297s 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 299s Processing target: p2-20_1 299s Keeping 6308 of 6646 bins 299s Correcting for GC bias... 299s Correcting for density bias... 299s Processing antitarget: p2-20_1 299s Keeping 12455 of 12563 bins 299s Correcting for GC bias... 299s WARNING: Skipping correction for RepeatMasker bias 299s Targets are 1.12 x more variable than antitargets 300s Wrote build/p2-20_1.cnr with 18763 regions 300s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 301s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 301s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 302s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 303s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 304s 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 306s Processing target: p2-20_2 306s Keeping 6308 of 6646 bins 306s Correcting for GC bias... 306s Correcting for density bias... 306s Processing antitarget: p2-20_2 306s Keeping 12455 of 12563 bins 306s Correcting for GC bias... 306s WARNING: Skipping correction for RepeatMasker bias 306s Targets are 1.10 x more variable than antitargets 307s Wrote build/p2-20_2.cnr with 18763 regions 307s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 308s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 309s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 309s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 311s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 311s 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 313s Processing target: p2-20_3 313s Keeping 6308 of 6646 bins 313s Correcting for GC bias... 313s Correcting for density bias... 313s Processing antitarget: p2-20_3 313s Keeping 12455 of 12563 bins 313s Correcting for GC bias... 313s WARNING: Skipping correction for RepeatMasker bias 314s Antitargets are 1.09 x more variable than targets 314s Wrote build/p2-20_3.cnr with 18763 regions 314s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 316s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 316s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 316s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 318s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 318s 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 320s Processing target: p2-20_4 320s Keeping 6308 of 6646 bins 320s Correcting for GC bias... 320s Correcting for density bias... 320s Processing antitarget: p2-20_4 320s Keeping 12455 of 12563 bins 321s Correcting for GC bias... 321s WARNING: Skipping correction for RepeatMasker bias 321s Targets are 1.43 x more variable than antitargets 321s Wrote build/p2-20_4.cnr with 18763 regions 321s 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 323s Processing target: p2-20_5 323s Keeping 6308 of 6646 bins 323s Correcting for GC bias... 323s Correcting for density bias... 323s Processing antitarget: p2-20_5 323s Keeping 12455 of 12563 bins 324s Correcting for GC bias... 324s WARNING: Skipping correction for RepeatMasker bias 324s Targets are 2.50 x more variable than antitargets 324s Wrote build/p2-20_5.cnr with 18763 regions 324s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 326s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 333s Dropped 8 / 49 bins on chromosome chrY 333s Wrote build/p2-5_5.cns with 71 regions 334s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 335s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 337s Dropped 1 / 949 bins on chromosome chr6 343s Dropped 27 / 49 bins on chromosome chrY 343s Wrote build/p2-9_2.cns with 103 regions 343s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 345s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 353s Dropped 6 / 49 bins on chromosome chrY 353s Wrote build/p2-20_1.cns with 121 regions 353s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 355s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 363s Dropped 7 / 49 bins on chromosome chrY 363s Wrote build/p2-20_2.cns with 117 regions 363s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 365s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 372s Dropped 11 / 49 bins on chromosome chrY 373s Wrote build/p2-20_3.cns with 64 regions 373s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 375s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 383s Dropped 8 / 49 bins on chromosome chrY 383s Wrote build/p2-20_4.cns with 143 regions 384s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 385s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 392s Smoothing overshot at 1 / 123 indices: (-0.3006003540408679, 0.3250888018519486) vs. original (-0.363302, 0.311218) 393s Dropped 6 / 49 bins on chromosome chrY 393s Wrote build/p2-20_5.cns with 120 regions 393s 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 397s Wrote p2-5_5-scatter.pdf 397s 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 399s Smoothing overshot at 3 / 97 indices: (-19.900105868621715, -3.3099069223720554) vs. original (-19.294, -0.16431) 401s Wrote p2-9_2-scatter.pdf 401s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 403s Showing 1480 probes and 0 selected genes in region chr1 403s Wrote p2-9_2-chr1-scatter.pdf 403s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 405s Showing 201 probes and 0 selected genes in region chr21 405s Wrote p2-9_2-chr21-scatter.pdf 406s 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 408s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 408s Wrote p2-9_2-chr9p-scatter.pdf 408s 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 410s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 411s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 411s 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 413s Detected file format: bed 413s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 413s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 414s 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 414s /usr/bin/pdfunite 414s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 416s Treating sample p2-5_5 as female 428s Wrote p2-5_5-diagram.pdf 428s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 430s Treating sample p2-9_2 as female 442s Wrote p2-9_2-diagram.pdf 442s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 444s Treating sample p2-20_1 as female 457s Wrote p2-20_1-diagram.pdf 457s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 459s Treating sample p2-20_2 as female 471s Wrote p2-20_2-diagram.pdf 471s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 473s Treating sample p2-5_5 as female 473s Wrote p2-5_5-cbs-diagram.pdf 473s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 474s Treating sample p2-9_2 as female 475s Wrote p2-9_2-cbs-diagram.pdf 475s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 476s Treating sample p2-20_1 as female 477s Wrote p2-20_1-cbs-diagram.pdf 477s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 478s Treating sample p2-20_2 as female 478s Wrote p2-20_2-cbs-diagram.pdf 479s 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 480s Treating sample p2-5_5 as female 490s 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 490s Wrote p2-5_5-both-diagram.pdf 490s Treating sample p2-9_2 as female 497s Wrote p2-9_2-both-diagram.pdf 498s 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 500s Treating sample p2-20_1 as female 509s Wrote p2-20_1-both-diagram.pdf 509s 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 511s Treating sample p2-20_2 as female 519s Wrote p2-20_2-both-diagram.pdf 519s 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 519s /usr/bin/pdfunite 519s 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 521s Treating sample p2-5_5 as female 521s Treating sample p2-9_2 as female 521s Treating sample p2-20_1 as female 521s Treating sample p2-20_2 as female 521s Treating sample p2-20_3 as female 521s Treating sample p2-20_4 as female 521s Treating sample p2-20_5 as female 523s Wrote heatmap-picard.pdf 524s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 526s Found 14 gene breakpoints 526s Wrote p2-9_2-breaks.txt 526s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 528s Treating sample p2-9_2 as female 530s Found 323 gene-level gains and losses 530s Wrote p2-9_2-genemetrics.txt 530s 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 532s Wrote gender-picard.txt 532s 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 539s Wrote p2-all.cdt 540s 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 547s Wrote p2-all-jtv.txt 547s 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 549s Wrote p2-all.seg 549s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 551s Wrote p2-9_2.nexus 552s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 554s Selected test sample NA12882 and control sample NA12878 554s Loaded 3654 records; skipped: 514 somatic, 394 depth 554s Kept 2631 heterozygous of 3654 VCF records 558s Placed 705 variants into 18763 bins 558s Wrote p2-9_2.nexus-ogt 558s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 560s Treating sample p2-5_5 as female 560s Rescaling sample with purity 0.65, ploidy 2 560s Wrote build/p2-5_5.call.cns with 71 regions 560s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 561s Treating sample p2-9_2 as female 561s Rescaling sample with purity 0.65, ploidy 2 561s Wrote build/p2-9_2.call.cns with 103 regions 562s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 563s Treating sample p2-20_1 as female 563s Rescaling sample with purity 0.65, ploidy 2 563s Wrote build/p2-20_1.call.cns with 121 regions 564s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 565s Treating sample p2-20_2 as female 565s Rescaling sample with purity 0.65, ploidy 2 565s Wrote build/p2-20_2.call.cns with 117 regions 565s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 567s Treating sample p2-20_3 as female 567s Rescaling sample with purity 0.65, ploidy 2 567s Wrote build/p2-20_3.call.cns with 64 regions 567s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 569s Treating sample p2-20_4 as female 569s Rescaling sample with purity 0.65, ploidy 2 569s Wrote build/p2-20_4.call.cns with 143 regions 569s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 571s Treating sample p2-20_5 as female 571s Rescaling sample with purity 0.65, ploidy 2 571s Wrote build/p2-20_5.call.cns with 120 regions 571s 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 573s Treating sample p2-5_5.call as female 573s Treating sample p2-9_2.call as female 573s Treating sample p2-20_1.call as female 573s Treating sample p2-20_2.call as female 573s Treating sample p2-20_3.call as female 573s Treating sample p2-20_4.call as female 573s Treating sample p2-20_5.call as female 573s Wrote p2-all.bed 573s 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 575s Treating sample p2-9_2.call as female 575s Wrote p2-9_2.vcf 576s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 577s /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)` 577s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 578s Wrote p2-9_2.theta2.input 578s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 578s --mean --median --mode --t-test \ 578s --stdev --mad --mse --iqr --bivar \ 578s --ci --pi --sem --smooth-bootstrap 581s Wrote p2-9_2-segmetrics.cns with 103 regions 581s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 581s --ci -b 50 -a 0.5 583s Wrote p2-5_5-segmetrics.cns with 71 regions 584s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 585s Wrote p2-5_5-metrics.tsv 586s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 587s Wrote p2-9_2-metrics.tsv 588s 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 590s Wrote p2-20-metrics.tsv 590s PASS 591s autopkgtest [11:15:42]: test run-unit-test: -----------------------] 591s run-unit-test PASS 591s autopkgtest [11:15:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 592s autopkgtest [11:15:43]: test pybuild-autopkgtest: preparing testbed 594s Reading package lists... 595s Building dependency tree... 595s Reading state information... 595s Starting pkgProblemResolver with broken count: 0 595s Starting 2 pkgProblemResolver with broken count: 0 595s Done 595s The following additional packages will be installed: 595s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 595s cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper debugedit 595s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 595s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 595s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 595s intltool-debian libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 595s libfile-stripnondeterminism-perl libgcc-14-dev libisl23 libitm1 liblsan0 595s libmpc3 libpython3.13-minimal libpython3.13-stdlib libquadmath0 595s libstdc++-14-dev libtool libtsan2 libubsan1 m4 po-debconf 595s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python3-all 595s python3-build python3-iniconfig python3-installer python3-pluggy 595s python3-pyproject-hooks python3-pytest python3-toml python3-wheel python3.13 595s python3.13-minimal 595s Suggested packages: 595s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 595s cpp-14-doc dh-make flit gcc-14-doc gcc-multilib manpages-dev flex bison gdb 595s gcc-doc gdb-powerpc64le-linux-gnu gettext-doc libasprintf-dev 595s libgettextpo-dev libstdc++-14-doc libtool-doc gfortran | fortran95-compiler 595s gcj-jdk m4-doc libmail-box-perl python3-pip python3-venv python-build-doc 595s python-installer-doc python3.13-venv python3.13-doc binfmt-support 595s Recommended packages: 595s libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 595s The following NEW packages will be installed: 595s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 595s cpp cpp-14 cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu debhelper 595s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 595s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 595s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext 595s intltool-debian libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 595s libfile-stripnondeterminism-perl libgcc-14-dev libisl23 libitm1 liblsan0 595s libmpc3 libpython3.13-minimal libpython3.13-stdlib libquadmath0 595s libstdc++-14-dev libtool libtsan2 libubsan1 m4 po-debconf 595s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python3-all 595s python3-build python3-iniconfig python3-installer python3-pluggy 595s python3-pyproject-hooks python3-pytest python3-toml python3-wheel python3.13 595s python3.13-minimal 595s 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. 595s Need to get 68.5 MB/68.6 MB of archives. 595s After this operation, 251 MB of additional disk space will be used. 595s Get:1 /tmp/autopkgtest.Z6Ak3I/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [864 B] 595s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 596s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 596s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB] 596s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB] 596s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB] 596s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] 596s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB] 596s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 596s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 596s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [10.5 MB] 596s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-8ubuntu1 [1034 B] 596s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B] 596s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB] 596s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-8ubuntu1 [48.1 kB] 596s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-8ubuntu1 [31.9 kB] 596s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-8ubuntu1 [2945 kB] 596s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-8ubuntu1 [1322 kB] 596s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-8ubuntu1 [2695 kB] 596s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-8ubuntu1 [1191 kB] 597s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-8ubuntu1 [158 kB] 597s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-8ubuntu1 [1619 kB] 597s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [20.6 MB] 597s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-8ubuntu1 [528 kB] 597s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B] 597s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B] 597s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-8ubuntu1 [2673 kB] 597s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [12.0 MB] 597s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-8ubuntu1 [19.9 kB] 597s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B] 597s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B] 597s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 597s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 597s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-7build1 [166 kB] 597s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB] 597s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] 597s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 597s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B] 597s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB] 597s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB] 597s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB] 598s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] 598s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] 598s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB] 598s Get:45 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20241024 [112 kB] 598s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 598s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 598s Get:48 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 598s Get:49 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB] 598s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-wheel all 0.44.0-1 [54.2 kB] 598s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-build all 1.2.2-1 [31.0 kB] 598s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 598s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pybuild-plugin-pyproject all 6.20241024 [1728 B] 598s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 598s Get:55 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 598s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 598s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 598s Get:58 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB] 598s Fetched 68.5 MB in 3s (26.8 MB/s) 598s Selecting previously unselected package libpython3.13-minimal:ppc64el. 598s (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 ... 90993 files and directories currently installed.) 598s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 598s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 598s Selecting previously unselected package python3.13-minimal. 598s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ... 598s Unpacking python3.13-minimal (3.13.0-2) ... 598s Selecting previously unselected package m4. 598s Preparing to unpack .../02-m4_1.4.19-4build1_ppc64el.deb ... 598s Unpacking m4 (1.4.19-4build1) ... 598s Selecting previously unselected package autoconf. 598s Preparing to unpack .../03-autoconf_2.72-3_all.deb ... 598s Unpacking autoconf (2.72-3) ... 599s Selecting previously unselected package autotools-dev. 599s Preparing to unpack .../04-autotools-dev_20220109.1_all.deb ... 599s Unpacking autotools-dev (20220109.1) ... 599s Selecting previously unselected package automake. 599s Preparing to unpack .../05-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 599s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 599s Selecting previously unselected package autopoint. 599s Preparing to unpack .../06-autopoint_0.22.5-2_all.deb ... 599s Unpacking autopoint (0.22.5-2) ... 599s Selecting previously unselected package libisl23:ppc64el. 599s Preparing to unpack .../07-libisl23_0.27-1_ppc64el.deb ... 599s Unpacking libisl23:ppc64el (0.27-1) ... 599s Selecting previously unselected package libmpc3:ppc64el. 599s Preparing to unpack .../08-libmpc3_1.3.1-1build2_ppc64el.deb ... 599s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 599s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 599s Preparing to unpack .../09-cpp-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 599s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 599s Selecting previously unselected package cpp-14. 599s Preparing to unpack .../10-cpp-14_14.2.0-8ubuntu1_ppc64el.deb ... 599s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 599s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 599s Preparing to unpack .../11-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 599s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 599s Selecting previously unselected package cpp. 599s Preparing to unpack .../12-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ... 599s Unpacking cpp (4:14.1.0-2ubuntu1) ... 599s Selecting previously unselected package libcc1-0:ppc64el. 599s Preparing to unpack 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599s Unpacking libubsan1:ppc64el (14.2.0-8ubuntu1) ... 600s Selecting previously unselected package libquadmath0:ppc64el. 600s Preparing to unpack .../19-libquadmath0_14.2.0-8ubuntu1_ppc64el.deb ... 600s Unpacking libquadmath0:ppc64el (14.2.0-8ubuntu1) ... 600s Selecting previously unselected package libgcc-14-dev:ppc64el. 600s Preparing to unpack .../20-libgcc-14-dev_14.2.0-8ubuntu1_ppc64el.deb ... 600s Unpacking libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ... 600s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 600s Preparing to unpack .../21-gcc-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ... 600s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ... 600s Selecting previously unselected package gcc-14. 600s Preparing to unpack .../22-gcc-14_14.2.0-8ubuntu1_ppc64el.deb ... 600s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 601s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 601s Preparing to unpack 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(4:14.1.0-2ubuntu1) ... 608s Setting up g++-14 (14.2.0-8ubuntu1) ... 608s Setting up g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ... 608s Setting up libtool (2.4.7-7build1) ... 608s Setting up gcc (4:14.1.0-2ubuntu1) ... 608s Setting up dh-autoreconf (20) ... 608s Setting up g++ (4:14.1.0-2ubuntu1) ... 608s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 608s Setting up build-essential (12.10ubuntu1) ... 608s Setting up debhelper (13.20ubuntu1) ... 608s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 608s Setting up autopkgtest-satdep (0) ... 608s Processing triggers for systemd (256.5-2ubuntu4) ... 608s Processing triggers for man-db (2.12.1-3) ... 609s Processing triggers for install-info (7.1.1-1) ... 609s Processing triggers for libc-bin (2.40-1ubuntu3) ... 613s (Reading database ... 94293 files and directories currently installed.) 613s Removing autopkgtest-satdep (0) ... 614s autopkgtest [11:16:05]: test pybuild-autopkgtest: pybuild-autopkgtest 614s autopkgtest [11:16:05]: test pybuild-autopkgtest: [----------------------- 615s pybuild-autopkgtest 615s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.Z6Ak3I/build.6cF/src/data /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/data; 615s I: pybuild base:311: cd /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build; python3.13 -m pytest test 616s ============================= test session starts ============================== 616s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 616s rootdir: /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build 616s configfile: pyproject.toml 616s plugins: typeguard-4.4.1 616s collected 0 items / 5 errors 616s 616s ==================================== ERRORS ==================================== 616s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 616s ImportError while importing test module '/tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/test/test_cnvlib.py'. 616s Hint: make sure your test modules/packages have valid Python names. 616s Traceback: 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 616s from . import multiarray 616s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 616s from . import overrides 616s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 616s from numpy.core._multiarray_umath import ( 616s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 616s 616s During handling of the above exception, another exception occurred: 616s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 616s from numpy.__config__ import show as show_config 616s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 616s from numpy.core._multiarray_umath import ( 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 616s raise ImportError(msg) 616s E ImportError: 616s E 616s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 616s E 616s E Importing the numpy C-extensions failed. This error can happen for 616s E many reasons, often due to issues with your setup or how NumPy was 616s E installed. 616s E 616s E We have compiled some common reasons and troubleshooting tips at: 616s E 616s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 616s E 616s E Please note and check the following: 616s E 616s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 616s E * The NumPy version is: "1.26.4" 616s E 616s E and make sure that they are the versions you expect. 616s E Please carefully study the documentation linked above for further help. 616s E 616s E Original error was: No module named 'numpy.core._multiarray_umath' 616s 616s The above exception was the direct cause of the following exception: 616s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 616s return _bootstrap._gcd_import(name[level:], package, level) 616s test/test_cnvlib.py:15: in 616s import numpy as np 616s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 616s raise ImportError(msg) from e 616s E ImportError: Error importing numpy: you should not try to import numpy from 616s E its source directory; please exit the numpy source tree, and relaunch 616s E your python interpreter from there. 616s ____________________ ERROR collecting test/test_commands.py ____________________ 616s ImportError while importing test module '/tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/test/test_commands.py'. 616s Hint: make sure your test modules/packages have valid Python names. 616s Traceback: 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 616s from . import multiarray 616s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 616s from . import overrides 616s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 616s from numpy.core._multiarray_umath import ( 616s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 616s 616s During handling of the above exception, another exception occurred: 616s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 616s from numpy.__config__ import show as show_config 616s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 616s from numpy.core._multiarray_umath import ( 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 616s raise ImportError(msg) 616s E ImportError: 616s E 616s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 616s E 616s E Importing the numpy C-extensions failed. This error can happen for 616s E many reasons, often due to issues with your setup or how NumPy was 616s E installed. 616s E 616s E We have compiled some common reasons and troubleshooting tips at: 616s E 616s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 616s E 616s E Please note and check the following: 616s E 616s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 616s E * The NumPy version is: "1.26.4" 616s E 616s E and make sure that they are the versions you expect. 616s E Please carefully study the documentation linked above for further help. 616s E 616s E Original error was: No module named 'numpy.core._multiarray_umath' 616s 616s The above exception was the direct cause of the following exception: 616s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 616s return _bootstrap._gcd_import(name[level:], package, level) 616s test/test_commands.py:16: in 616s import numpy as np 616s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 616s raise ImportError(msg) from e 616s E ImportError: Error importing numpy: you should not try to import numpy from 616s E its source directory; please exit the numpy source tree, and relaunch 616s E your python interpreter from there. 616s _____________________ ERROR collecting test/test_genome.py _____________________ 616s ImportError while importing test module '/tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/test/test_genome.py'. 616s Hint: make sure your test modules/packages have valid Python names. 616s Traceback: 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:24: in 616s from . import multiarray 616s /usr/lib/python3/dist-packages/numpy/core/multiarray.py:10: in 616s from . import overrides 616s /usr/lib/python3/dist-packages/numpy/core/overrides.py:8: in 616s from numpy.core._multiarray_umath import ( 616s E ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 616s 616s During handling of the above exception, another exception occurred: 616s /usr/lib/python3/dist-packages/numpy/__init__.py:130: in 616s from numpy.__config__ import show as show_config 616s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 616s from numpy.core._multiarray_umath import ( 616s /usr/lib/python3/dist-packages/numpy/core/__init__.py:50: in 616s raise ImportError(msg) 616s E ImportError: 616s E 616s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 616s E 616s E Importing the numpy C-extensions failed. This error can happen for 616s E many reasons, often due to issues with your setup or how NumPy was 616s E installed. 616s E 616s E We have compiled some common reasons and troubleshooting tips at: 616s E 616s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 616s E 616s E Please note and check the following: 616s E 616s E * The Python version is: Python3.13 from "/usr/bin/python3.13" 616s E * The NumPy version is: "1.26.4" 616s E 616s E and make sure that they are the versions you expect. 616s E Please carefully study the documentation linked above for further help. 616s E 616s E Original error was: No module named 'numpy.core._multiarray_umath' 616s 616s The above exception was the direct cause of the following exception: 616s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 616s return _bootstrap._gcd_import(name[level:], package, level) 616s test/test_genome.py:12: in 616s import numpy as np 616s /usr/lib/python3/dist-packages/numpy/__init__.py:135: in 616s raise ImportError(msg) from e 616s E ImportError: Error importing numpy: you should not try to import numpy from 616s E its source directory; please exit the numpy source tree, and relaunch 616s E your python interpreter from there. 616s _______________________ ERROR collecting test/test_io.py _______________________ 616s ImportError while importing test module '/tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/test/test_io.py'. 616s Hint: make sure your test modules/packages have valid Python names. 616s Traceback: 616s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 616s return _bootstrap._gcd_import(name[level:], package, level) 616s test/test_io.py:11: in 616s from skgenome import tabio 616s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 616s from . import tabio 616s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 616s import pandas as pd 616s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 616s raise ImportError( 616s E ImportError: Unable to import required dependencies: 616s E numpy: Error importing numpy: you should not try to import numpy from 616s E its source directory; please exit the numpy source tree, and relaunch 616s E your python interpreter from there. 616s _______________________ ERROR collecting test/test_r.py ________________________ 616s ImportError while importing test module '/tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/test/test_r.py'. 616s Hint: make sure your test modules/packages have valid Python names. 616s Traceback: 616s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 616s return _bootstrap._gcd_import(name[level:], package, level) 616s test/test_r.py:14: in 616s import cnvlib 616s /usr/lib/python3/dist-packages/cnvlib/__init__.py:1: in 616s from skgenome.tabio import write 616s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 616s from . import tabio 616s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 616s import pandas as pd 616s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 616s raise ImportError( 616s E ImportError: Unable to import required dependencies: 616s E numpy: Error importing numpy: you should not try to import numpy from 616s E its source directory; please exit the numpy source tree, and relaunch 616s E your python interpreter from there. 616s =========================== short test summary info ============================ 616s ERROR test/test_cnvlib.py 616s ERROR test/test_commands.py 616s ERROR test/test_genome.py 616s ERROR test/test_io.py 616s ERROR test/test_r.py 616s !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! 616s ============================== 5 errors in 0.42s =============================== 616s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build; python3.13 -m pytest test 616s I: pybuild pybuild:308: ln -s /tmp/autopkgtest.Z6Ak3I/build.6cF/src/data /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build/data; 616s I: pybuild base:311: cd /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build; python3.12 -m pytest test 619s ============================= test session starts ============================== 619s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 619s rootdir: /tmp/autopkgtest.Z6Ak3I/autopkgtest_tmp/build 619s configfile: pyproject.toml 619s plugins: typeguard-4.4.1 619s collected 64 items 619s 626s test/test_cnvlib.py ......... [ 14%] 655s test/test_commands.py ......................... [ 53%] 662s test/test_genome.py ................... [ 82%] 663s test/test_io.py .......... [ 98%] 675s test/test_r.py . [100%] 675s 675s =============================== warnings summary =============================== 675s test/test_commands.py::CommandTests::test_antitarget 675s test/test_commands.py::CommandTests::test_target 675s test/test_genome.py::GaryTests::test_ranges_resize 675s test/test_io.py::IOTests::test_empty 675s test/test_io.py::IOTests::test_read_auto 675s test/test_io.py::IOTests::test_read_auto 675s test/test_io.py::IOTests::test_read_ilist 675s /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. 675s 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. 675s 675s 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. 675s 675s 675s dframe["gene"].fillna("-", inplace=True) 675s 675s test/test_commands.py: 11 warnings 675s test/test_genome.py: 6 warnings 675s /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. 675s .apply(_merge_overlapping, bp, cmb) 675s 675s test/test_commands.py::CommandTests::test_batch 675s /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. 675s 0. 0. 0. 0. 0. 0. 675s 0. 0. 0. 0. 0. 0. 675s 0. 0. 0. 1.20240481 0.31062124 0.89178357 675s 0. 0. 0. 1.20240481 0.4 0.2004008 675s 0. 0.4008016 0.4 0.4008016 0. 0. 675s 0. 0.4008016 0. 1.20240481 0. 0. 675s 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 675s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 675s 675s test/test_commands.py::CommandTests::test_batch 675s test/test_commands.py::CommandTests::test_batch 675s /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. 675s ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) 675s 675s test/test_commands.py::CommandTests::test_batch 675s test/test_commands.py::CommandTests::test_batch 675s /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. 675s 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 675s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 675s 675s test/test_commands.py: 19 warnings 675s /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. 675s .apply(squash_region) 675s 675s test/test_commands.py: 10 warnings 675s /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)` 675s chrom_col = cnarr["chromosome"].replace( 675s 675s test/test_commands.py::CommandTests::test_coverage 675s test/test_commands.py::CommandTests::test_coverage 675s test/test_commands.py::CommandTests::test_coverage 675s test/test_commands.py::CommandTests::test_coverage 675s /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. 675s table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] 675s 675s test/test_commands.py::CommandTests::test_export_theta 675s test/test_commands.py::CommandTests::test_export_theta 675s /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)` 675s table["chrm"] = tumor_segs.chromosome.replace(chr2idx) 675s 675s test/test_commands.py: 8 warnings 675s test/test_genome.py: 21 warnings 675s /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. 675s table = pd.DataFrame.from_records(rows, columns=columns) 675s 675s test/test_commands.py::CommandTests::test_target 675s test/test_commands.py::CommandTests::test_target 675s test/test_commands.py::CommandTests::test_target 675s test/test_commands.py::CommandTests::test_target 675s test/test_commands.py::CommandTests::test_target 675s test/test_commands.py::CommandTests::test_target 675s test/test_genome.py::GaryTests::test_total_range_size 675s test/test_genome.py::GaryTests::test_total_range_size 675s /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. 675s return sep.join(pd.unique(elems)) 675s 675s test/test_genome.py::GaryTests::test_ranges_resize 675s /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)` 675s limits["upper"] = self.chromosome.replace(chrom_sizes) 675s 675s test/test_genome.py::IntervalTests::test_flatten 675s test/test_genome.py::IntervalTests::test_flatten 675s /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. 675s .apply(_flatten_overlapping, cmb, split_columns) 675s 675s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 675s ====================== 64 passed, 104 warnings in 58.61s ======================= 675s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 675s make: *** [/tmp/AM4PSJYt6a/run:4: pybuild-autopkgtest] Error 25 675s pybuild-autopkgtest: error: /tmp/AM4PSJYt6a/run pybuild-autopkgtest returned exit code 2 676s autopkgtest [11:17:07]: test pybuild-autopkgtest: -----------------------] 676s autopkgtest [11:17:07]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 676s pybuild-autopkgtest FAIL non-zero exit status 25 676s autopkgtest [11:17:07]: @@@@@@@@@@@@@@@@@@@@ summary 676s run-unit-test PASS 676s pybuild-autopkgtest FAIL non-zero exit status 25 682s nova [W] Using flock in prodstack6-ppc64el 682s Creating nova instance adt-plucky-ppc64el-cnvkit-20241113-110551-juju-7f2275-prod-proposed-migration-environment-15-61e2f1fc-a768-4994-aaf8-381a4c9db638 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...