https://launchpad.net/ubuntu/+source/cnvkit/0.9.9-2/+build/22292071 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-005 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:41:12 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_203~505~ubuntu18.04.1 python3-lpbuildd_203~505~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 22 Oct 11:40:50 ntpdate[1724]: adjust time server 10.211.37.1 offset 0.002641 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292071 --image-type chroot /home/buildd/filecache-default/d7d0133902b8cc1df688a841d4b96e994eeac2e0 Creating target for build PACKAGEBUILD-22292071 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292071 Starting target for build PACKAGEBUILD-22292071 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292071 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22292071 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292071 Updating target for build PACKAGEBUILD-22292071 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 Packages [1371 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe arm64 Packages [13.0 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5503 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 Packages [359 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [121 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 Packages [1818 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [917 kB] Fetched 24.0 MB in 10s (2387 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bsdutils ca-certificates cpp-11 debianutils g++-11 gcc-11 gcc-11-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libblkid1 libcc1-0 libgcc-11-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgomp1 libgpg-error0 libgssapi-krb5-2 libhwasan0 libidn2-0 libisl23 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libtsan0 libubsan1 libuuid1 libzstd1 lockfile-progs make mount ncurses-base ncurses-bin sensible-utils util-linux 54 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 182 MB of archives. After this operation, 33.8 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 bsdutils arm64 1:2.36.1-8ubuntu2 [81.0 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 debianutils arm64 5.5-1 [77.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libncursesw6 arm64 6.2+20210905-1 [142 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libncurses6 arm64 6.2+20210905-1 [108 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libtinfo6 arm64 6.2+20210905-1 [104 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 ncurses-bin arm64 6.2+20210905-1 [180 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 util-linux arm64 2.36.1-8ubuntu2 [1004 kB] Get:8 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 ncurses-base all 6.2+20210905-1 [19.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libcc1-0 arm64 11.2.0-10ubuntu1 [54.2 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 gcc-11-base arm64 11.2.0-10ubuntu1 [21.0 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgcc-s1 arm64 11.2.0-10ubuntu1 [39.3 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgomp1 arm64 11.2.0-10ubuntu1 [115 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libitm1 arm64 11.2.0-10ubuntu1 [28.4 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libatomic1 arm64 11.2.0-10ubuntu1 [10.9 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libasan6 arm64 11.2.0-10ubuntu1 [2228 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 liblsan0 arm64 11.2.0-10ubuntu1 [942 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libtsan0 arm64 11.2.0-10ubuntu1 [2233 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libubsan1 arm64 11.2.0-10ubuntu1 [908 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libhwasan0 arm64 11.2.0-10ubuntu1 [1010 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 g++-11 arm64 11.2.0-10ubuntu1 [54.4 MB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libstdc++-11-dev arm64 11.2.0-10ubuntu1 [2064 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgcc-11-dev arm64 11.2.0-10ubuntu1 [1149 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 gcc-11 arm64 11.2.0-10ubuntu1 [58.3 MB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 cpp-11 arm64 11.2.0-10ubuntu1 [50.0 MB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libstdc++6 arm64 11.2.0-10ubuntu1 [623 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libisl23 arm64 0.24-2 [690 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libmpc3 arm64 1.2.1-1 [48.1 kB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libzstd1 arm64 1.4.8+dfsg-3 [311 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libapt-pkg6.0 arm64 2.3.11 [864 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libseccomp2 arm64 2.5.1-1ubuntu2 [47.8 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 apt arm64 2.3.11 [1356 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 mount arm64 2.36.1-8ubuntu2 [109 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libattr1 arm64 1:2.5.1-1 [13.3 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libblkid1 arm64 2.36.1-8ubuntu2 [97.8 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgpg-error0 arm64 1.42-3 [67.7 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libk5crypto3 arm64 1.18.3-7 [91.5 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libkrb5support0 arm64 1.18.3-7 [32.3 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libkrb5-3 arm64 1.18.3-7 [357 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgssapi-krb5-2 arm64 1.18.3-7 [141 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libselinux1 arm64 3.1-3build3 [74.1 kB] Get:41 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libmount1 arm64 2.36.1-8ubuntu2 [115 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsmartcols1 arm64 2.36.1-8ubuntu2 [48.5 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libuuid1 arm64 2.36.1-8ubuntu2 [23.2 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libidn2-0 arm64 2.3.2-2 [67.1 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libp11-kit0 arm64 0.24.0-5 [231 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libtasn1-6 arm64 4.17.0-2 [42.8 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 sensible-utils all 0.0.17 [20.1 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 ca-certificates all 20211016 [148 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libapparmor1 arm64 3.0.3-0ubuntu2 [37.4 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsqlite3-0 arm64 3.36.0-2 [638 kB] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgdbm6 arm64 1.22-1 [35.1 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgdbm-compat4 arm64 1.22-1 [6370 B] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 lockfile-progs arm64 0.1.19 [9778 B] Get:54 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 make arm64 4.3-4ubuntu2 [176 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 182 MB in 25s (7354 kB/s) (Reading database ... 13240 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.36.1-8ubuntu2_arm64.deb ... Unpacking bsdutils (1:2.36.1-8ubuntu2) over (1:2.36.1-8ubuntu1) ... Setting up bsdutils (1:2.36.1-8ubuntu2) ... (Reading database ... 13240 files and directories currently installed.) Preparing to unpack .../debianutils_5.5-1_arm64.deb ... Unpacking debianutils (5.5-1) over (4.11.2build1) ... Setting up debianutils (5.5-1) ... update-alternatives: using /usr/bin/which.debianutils to provide /usr/bin/which (which) in auto mode (Reading database ... 13235 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.2+20210905-1_arm64.deb ... Unpacking libncursesw6:arm64 (6.2+20210905-1) over (6.2+20201114-2build2) ... Preparing to unpack .../libncurses6_6.2+20210905-1_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20210905-1) over (6.2+20201114-2build2) ... Preparing to unpack .../libtinfo6_6.2+20210905-1_arm64.deb ... Unpacking libtinfo6:arm64 (6.2+20210905-1) over (6.2+20201114-2build2) ... 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Unpacking libapparmor1:arm64 (3.0.3-0ubuntu2) over (3.0.3-0ubuntu1) ... Preparing to unpack .../3-libsqlite3-0_3.36.0-2_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.36.0-2) over (3.35.5-1) ... Preparing to unpack .../4-libgdbm6_1.22-1_arm64.deb ... Unpacking libgdbm6:arm64 (1.22-1) over (1.19-2build1) ... Preparing to unpack .../5-libgdbm-compat4_1.22-1_arm64.deb ... Unpacking libgdbm-compat4:arm64 (1.22-1) over (1.19-2build1) ... Preparing to unpack .../6-lockfile-progs_0.1.19_arm64.deb ... Unpacking lockfile-progs (0.1.19) over (0.1.18build1) ... Preparing to unpack .../7-make_4.3-4ubuntu2_arm64.deb ... Unpacking make (4.3-4ubuntu2) over (4.3-4ubuntu1) ... Setting up libapparmor1:arm64 (3.0.3-0ubuntu2) ... Setting up libsqlite3-0:arm64 (3.36.0-2) ... Setting up libgomp1:arm64 (11.2.0-10ubuntu1) ... Setting up libasan6:arm64 (11.2.0-10ubuntu1) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:arm64 (6.2+20210905-1) ... Setting up libmpc3:arm64 (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:arm64 (11.2.0-10ubuntu1) ... Setting up libncursesw6:arm64 (6.2+20210905-1) ... Setting up libubsan1:arm64 (11.2.0-10ubuntu1) ... Setting up mount (2.36.1-8ubuntu2) ... Setting up sensible-utils (0.0.17) ... Setting up libhwasan0:arm64 (11.2.0-10ubuntu1) ... Setting up libisl23:arm64 (0.24-2) ... Setting up libcc1-0:arm64 (11.2.0-10ubuntu1) ... Setting up liblsan0:arm64 (11.2.0-10ubuntu1) ... Setting up libitm1:arm64 (11.2.0-10ubuntu1) ... Setting up libgdbm6:arm64 (1.22-1) ... Setting up libtsan0:arm64 (11.2.0-10ubuntu1) ... Setting up cpp-11 (11.2.0-10ubuntu1) ... Setting up libgdbm-compat4:arm64 (1.22-1) ... Setting up libgcc-11-dev:arm64 (11.2.0-10ubuntu1) ... Setting up gcc-11 (11.2.0-10ubuntu1) ... Setting up libstdc++-11-dev:arm64 (11.2.0-10ubuntu1) ... Setting up g++-11 (11.2.0-10ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22292071 arm64 jammy-proposed -c chroot:build-PACKAGEBUILD-22292071 --arch=arm64 --dist=jammy-proposed --nolog cnvkit_0.9.9-2.dsc Initiating build PACKAGEBUILD-22292071 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:41:12 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-005.buildd +==============================================================================+ | cnvkit 0.9.9-2 (arm64) Fri, 22 Oct 2021 11:42:30 +0000 | +==============================================================================+ Package: cnvkit Version: 0.9.9-2 Source Version: 0.9.9-2 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22292071/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cnvkit_0.9.9-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/cnvkit-3s4tZ5/cnvkit-0.9.9' with '<>' I: NOTICE: Log filtering will replace 'build/cnvkit-3s4tZ5' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-Ctj0i6/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-Ctj0i6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Ctj0i6/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-Ctj0i6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Ctj0i6/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-Ctj0i6/apt_archive ./ Packages [432 B] Fetched 1738 B in 0s (21.6 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 650 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Ctj0i6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [650 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 650 B in 0s (43.2 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13242 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in amd64 arm64 ppc64el) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, r-bioc-dnacopy, poppler-utils Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-pyfaidx, help2man, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pyvcf, python3-future, python3-pomegranate, r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'sbuild-build-depends-cnvkit-dummy' in '/<>/resolver-Ctj0i6/apt_archive/sbuild-build-depends-cnvkit-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-cnvkit-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-Ctj0i6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Ctj0i6/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-Ctj0i6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Ctj0i6/apt_archive ./ Sources [604 B] Get:5 copy:/<>/resolver-Ctj0i6/apt_archive ./ Packages [680 B] Fetched 2247 B in 0s (44.8 kB/s) Reading package lists... Reading package lists... Install cnvkit build dependencies (apt-based resolver) ------------------------------------------------------ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx fonts-urw-base35 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler111 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 mailcap man-db media-types mime-support po-debconf poppler-utils python-matplotlib-data python3 python3-all python3-biopython python3-cycler python3-dateutil python3-decorator python3-distutils python3-future python3-joblib python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-vcf python3-yaml python3.10 python3.10-minimal python3.9 python3.9-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy ttf-bitstream-vera ucf unzip x11-common xdg-utils zip Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-toml fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml samtools t-coffee wise w3-dtd-mathml python-cycler-doc python-future-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-networkx-doc python3-gdal python3-pydot python3-pygraphviz gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pandas-doc python3-statsmodels python-pil-doc python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support python3.9-venv python3.9-doc elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common poppler-data publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-tk python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-olefile r-recommended r-base-dev r-doc-html r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx fonts-urw-base35 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libmpdec3 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler111 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.9-minimal libpython3.9-stdlib libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 mailcap man-db media-types mime-support po-debconf poppler-utils python-matplotlib-data python3 python3-all python3-biopython python3-cycler python3-dateutil python3-decorator python3-distutils python3-future python3-joblib python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-vcf python3-yaml python3.10 python3.10-minimal python3.9 python3.9-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy sbuild-build-depends-cnvkit-dummy ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 166 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 449 MB of additional disk space will be used. Get:1 copy:/<>/resolver-Ctj0i6/apt_archive ./ sbuild-build-depends-cnvkit-dummy 0.invalid.0 [760 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 liblocale-gettext-perl arm64 1.07-4build2 [17.0 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3.9-minimal arm64 3.9.7-4 [781 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 libexpat1 arm64 2.4.1-2 [75.9 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3.9-minimal arm64 3.9.7-4 [2112 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-minimal arm64 3.9.4-1ubuntu2 [24.6 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 media-types all 4.0.0 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 mailcap all 3.70ubuntu1 [23.7 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 mime-support all 3.66 [3696 B] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpdec3 arm64 2.5.1-2build1 [89.0 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3.9-stdlib arm64 3.9.7-4 [1803 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3.9 arm64 3.9.7-4 [433 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libpython3-stdlib arm64 3.9.4-1ubuntu2 [7186 B] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3 arm64 3.9.4-1ubuntu2 [22.8 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 bsdextrautils arm64 2.36.1-8ubuntu2 [73.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 libuchardet0 arm64 0.0.7-1build1 [76.8 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main arm64 groff-base arm64 1.22.4-7 [918 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 libpipeline1 arm64 1.5.3-1build1 [22.9 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 man-db arm64 2.9.4-2build1 [1175 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 libpython3.10-minimal arm64 3.10.0-3 [799 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main arm64 python3.10-minimal arm64 3.10.0-3 [2162 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libmd0 arm64 1.0.4-1 [23.8 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 libbsd0 arm64 0.11.3-1ubuntu3 [43.5 kB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libelf1 arm64 0.185-2 [51.1 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 libfribidi0 arm64 1.0.8-2ubuntu2 [26.1 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 libglib2.0-0 arm64 2.68.4-1ubuntu1 [1392 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 libicu67 arm64 67.1-7ubuntu1 [10.0 MB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libxml2 arm64 2.9.12+dfsg-5 [725 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 libyaml-0-2 arm64 0.2.2-1build1 [51.1 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-pkg-resources all 58.2.0-1 [130 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 python3-yaml arm64 5.4.1-1 [159 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 ucf all 3.0043 [56.1 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic-mgc arm64 1:5.39-3build1 [236 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic1 arm64 1:5.39-3build1 [87.8 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main arm64 file arm64 1:5.39-3build1 [24.7 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext-base arm64 0.21-4ubuntu3 [35.2 kB] Get:37 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libedit2 arm64 3.1-20210910-1 [95.9 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main arm64 libpsl5 arm64 0.21.0-1.2build1 [57.5 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main arm64 libxau6 arm64 1:1.0.9-1build4 [7638 B] Get:40 http://ftpmaster.internal/ubuntu jammy/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu4 [10.9 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 libxcb1 arm64 1.14-3ubuntu2 [49.1 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libx11-data all 2:1.7.2-2 [123 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libx11-6 arm64 2:1.7.2-2 [659 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main arm64 libxext6 arm64 2:1.3.4-0ubuntu4 [30.6 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main arm64 libsigsegv2 arm64 2.13-1ubuntu2 [14.5 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 m4 arm64 1.4.18-5ubuntu1 [196 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 autoconf all 2.71-2 [338 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main arm64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main arm64 automake all 1:1.16.4-2 [557 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main arm64 autopoint all 0.21-4ubuntu3 [422 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main arm64 libdebhelper-perl all 13.3.4ubuntu2 [62.5 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main arm64 libtool all 2.4.6-15build1 [164 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main arm64 dh-autoreconf all 20 [16.1 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libfile-stripnondeterminism-perl all 1.12.0-2 [18.0 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 dh-strip-nondeterminism all 1.12.0-2 [5208 B] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libdw1 arm64 0.185-2 [244 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main arm64 debugedit arm64 1:5.0-0ubuntu2 [47.0 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main arm64 dwz arm64 0.14-1build1 [102 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext arm64 0.21-4ubuntu3 [775 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main arm64 debhelper all 13.3.4ubuntu2 [921 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main arm64 python3-lib2to3 all 3.9.7-1 [77.9 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main arm64 python3-distutils all 3.9.7-1 [144 kB] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 dh-python all 5.20211021 [99.5 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main arm64 libbrotli1 arm64 1.0.9-2build4 [314 kB] Get:69 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libfreetype6 arm64 2.11.0+dfsg-1 [382 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/universe arm64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main arm64 fonts-urw-base35 all 20200910-1 [6367 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main arm64 fontconfig-config all 2.13.1-4.2ubuntu4 [29.1 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main arm64 libfontconfig1 arm64 2.13.1-4.2ubuntu4 [135 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main arm64 fontconfig arm64 2.13.1-4.2ubuntu4 [183 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/universe arm64 fonts-lyx all 2.3.6-1 [159 kB] Get:76 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 help2man arm64 1.48.5 [139 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main arm64 libblas3 arm64 3.9.0-3ubuntu3 [138 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main arm64 libpixman-1-0 arm64 0.40.0-1build3 [160 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main arm64 libxcb-render0 arm64 1.14-3ubuntu2 [16.3 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main arm64 libxcb-shm0 arm64 1.14-3ubuntu2 [5862 B] 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Setting up libmagic-mgc (1:5.39-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.2-1build1) ... Setting up libglib2.0-0:arm64 (2.68.4-1ubuntu1) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up unzip (6.0-26ubuntu2) ... Setting up libdebhelper-perl (13.3.4ubuntu2) ... Setting up libbrotli1:arm64 (1.0.9-2build4) ... Setting up x11-common (1:7.7+23ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:arm64 (1.43.0-1build1) ... Setting up libmagic1:arm64 (1:5.39-3build1) ... Setting up libdeflate0:arm64 (1.7-2ubuntu2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.39-3build1) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up libjbig0:arm64 (2.1-3.1build2) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1build1) ... Setting up zip (3.0-12build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:arm64 (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libfreetype6:arm64 (2.11.0+dfsg-1) ... Setting up libx11-data (2:1.7.2-2) ... Setting up libnspr4:arm64 (2:4.32-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build3) ... Setting up libsigsegv2:arm64 (2.13-1ubuntu2) ... Setting up libfribidi0:arm64 (1.0.8-2ubuntu2) ... Setting up libimagequant0:arm64 (2.12.2-1.1build1) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1build1) ... Setting up libpython3.10-minimal:arm64 (3.10.0-3) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up libwebp6:arm64 (0.6.1-2.1build1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:arm64 (2.0.6-0ubuntu3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1build1) ... Setting up libssh-4:arm64 (0.9.6-1) ... Setting up libgfortran5:arm64 (11.2.0-10ubuntu1) ... 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Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-1build1) ... Setting up libdw1:arm64 (0.185-2) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu4) ... Setting up liblapack3:arm64 (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-3ubuntu2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15build1) ... Setting up libxcb-render0:arm64 (1.14-3ubuntu2) ... Setting up fontconfig-config (2.13.1-4.2ubuntu4) ... Setting up libwebpdemux2:arm64 (0.6.1-2.1build1) ... Setting up libedit2:arm64 (3.1-20210910-1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libnss3:arm64 (2:3.68-1ubuntu1) ... Setting up libxcb-shm0:arm64 (1.14-3ubuntu2) ... Setting up libpaper-utils (1.1.28build1) ... Setting up python3.10-minimal (3.10.0-3) ... Setting up libldap-2.5-0:arm64 (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.5) ... Setting up libpython3.10-stdlib:arm64 (3.10.0-3) ... Setting up libthai0:arm64 (0.1.28-4.1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libraqm0:arm64 (0.7.0-4) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up libcurl4:arm64 (7.74.0-1.3ubuntu2) ... Setting up libx11-6:arm64 (2:1.7.2-2) ... Setting up libtiff5:arm64 (4.3.0-2) ... Setting up libfontconfig1:arm64 (2.13.1-4.2ubuntu4) ... Setting up libsm6:arm64 (2:1.2.3-1build1) ... Setting up python3.9 (3.9.7-4) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.3-9) ... Setting up automake (1:1.16.4-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpoppler111:arm64 (21.06.1-1) ... Setting up fontconfig (2.13.1-4.2ubuntu4) ... Regenerating fonts cache... done. Setting up python3.10 (3.10.0-3) ... Setting up libxrender1:arm64 (1:0.9.10-1build3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.48.10+ds1-1) ... Setting up libxext6:arm64 (2:1.3.4-0ubuntu4) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3ubuntu2) ... Setting up python3 (3.9.4-1ubuntu2) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libcairo2:arm64 (1.16.0-5ubuntu2) ... Setting up python3-tz (2021.3-1) ... Setting up python3-six (1.16.0-2) ... Setting up dh-autoreconf (20) ... Setting up python3-pil:arm64 (8.3.2-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:arm64 (3.6.1-1) ... Setting up python3-kiwisolver (1.3.2-1) ... Setting up libxt6:arm64 (1:1.2.0-1build1) ... Setting up python3-reportlab (3.6.1-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:arm64 (1:1.2.3-1build1) ... Setting up poppler-utils (21.06.1-1) ... Setting up libpangoft2-1.0-0:arm64 (1.48.10+ds1-1) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up libpangocairo-1.0-0:arm64 (1.48.10+ds1-1) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up dh-python (5.20211021) ... Setting up python3-pyfaidx (0.6.2-1) ... Setting up libxft2:arm64 (2.3.3-0ubuntu4) ... Setting up libhts3:arm64 (1.13+ds-2) ... Setting up python3-pysam (0.17.0+ds-2) ... Setting up python3-renderpm:arm64 (3.6.1-1) ... Setting up python3-setuptools (58.2.0-1) ... Setting up python3-joblib (0.17.0-4) ... Setting up libtk8.6:arm64 (8.6.11.1-1) ... Setting up python3-all (3.9.4-1ubuntu2) ... Setting up python3-yaml (5.4.1-1) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up python3-networkx (2.4-4ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up python3-vcf (0.6.8+git20170215.476169c-8) ... Setting up r-base-core (4.1.1-2) ... Creating config file /etc/R/Renviron with new version Setting up python3-numpy (1:1.20.2-1ubuntu1) ... Setting up python3-future (0.18.2-5) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.78+dfsg-5ubuntu1) ... Setting up python3-matplotlib (3.3.4-2) ... Setting up r-bioc-biocgenerics (0.38.0-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pomegranate (0.13.5-1) ... Setting up python3-pandas-lib:arm64 (1.1.5+dfsg-2) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up r-bioc-dnacopy (1.66.0-1) ... Setting up sbuild-build-depends-cnvkit-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-161-generic arm64 (aarch64) Toolchain package versions: binutils_2.37-7ubuntu1 dpkg-dev_1.20.9ubuntu2 g++-11_11.2.0-10ubuntu1 gcc-11_11.2.0-10ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-10ubuntu1 libstdc++6_11.2.0-10ubuntu1 linux-libc-dev_5.13.0-19.19 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu1 base-passwd_3.5.52 bash_5.1-3ubuntu2 binutils_2.37-7ubuntu1 binutils-aarch64-linux-gnu_2.37-7ubuntu1 binutils-common_2.37-7ubuntu1 bsdextrautils_2.36.1-8ubuntu2 bsdutils_1:2.36.1-8ubuntu2 build-essential_12.9ubuntu2 bzip2_1.0.8-4ubuntu4 ca-certificates_20211016 coreutils_8.32-4ubuntu3 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libjbig0_2.1-3.1build2 libjpeg-turbo8_2.0.6-0ubuntu3 libjpeg8_8c-2ubuntu8 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjson-c5_0.15-2build3 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2ubuntu2 libkmod2_28-1ubuntu4 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 liblapack3_3.9.0-3ubuntu3 liblbfgsb0_3.0+dfsg.3-9 liblcms2-2_2.12~rc1-2build1 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-4build2 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblsan0_11.2.0-10ubuntu1 liblz4-1_1.9.3-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.39-3build1 libmagic1_1:5.39-3build1 libmd0_1.0.4-1 libmount1_2.36.1-8ubuntu2 libmpc3_1.2.1-1 libmpdec3_2.5.1-2build1 libmpfr6_4.1.0-3build2 libncurses6_6.2+20210905-1 libncursesw6_6.2+20210905-1 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build1 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libnspr4_2:4.32-1 libnss3_2:3.68-1ubuntu1 libopenjp2-7_2.4.0-3 libp11-kit0_0.24.0-5 libpam-modules_1.3.1-5ubuntu11 libpam-modules-bin_1.3.1-5ubuntu11 libpam-runtime_1.3.1-5ubuntu11 libpam0g_1.3.1-5ubuntu11 libpango-1.0-0_1.48.10+ds1-1 libpangocairo-1.0-0_1.48.10+ds1-1 libpangoft2-1.0-0_1.48.10+ds1-1 libpaper-utils_1.1.28build1 libpaper1_1.1.28build1 libpcre2-8-0_10.37-0ubuntu2 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.3-1build1 libpixman-1-0_0.40.0-1build3 libpng16-16_1.6.37-3build4 libpoppler111_21.06.1-1 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libpython3-stdlib_3.9.4-1ubuntu2 libpython3.10-minimal_3.10.0-3 libpython3.10-stdlib_3.10.0-3 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libraqm0_0.7.0-4 libreadline8_8.1-2build1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libsasl2-2_2.1.27+dfsg-2.1build1 libsasl2-modules-db_2.1.27+dfsg-2.1build1 libseccomp2_2.5.1-1ubuntu2 libselinux1_3.1-3build3 libsemanage-common_3.1-1ubuntu3 libsemanage1_3.1-1ubuntu3 libsepol1_3.1-1ubuntu2 libsigsegv2_2.13-1ubuntu2 libsm6_2:1.2.3-1build1 libsmartcols1_2.36.1-8ubuntu2 libsqlite3-0_3.36.0-2 libss2_1.46.3-1ubuntu3 libssh-4_0.9.6-1 libssl1.1_1.1.1l-1ubuntu1 libstdc++-11-dev_11.2.0-10ubuntu1 libstdc++6_11.2.0-10ubuntu1 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu8 libtasn1-6_4.17.0-2 libtcl8.6_8.6.11+dfsg-1build1 libthai-data_0.1.28-4.1 libthai0_0.1.28-4.1 libtiff5_4.3.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtk8.6_8.6.11.1-1 libtool_2.4.6-15build1 libtsan0_11.2.0-10ubuntu1 libubsan1_11.2.0-10ubuntu1 libuchardet0_0.0.7-1build1 libudev1_248.3-1ubuntu8 libunistring2_0.9.10-6 libuuid1_2.36.1-8ubuntu2 libwebp6_0.6.1-2.1build1 libwebpdemux2_0.6.1-2.1build1 libwebpmux3_0.6.1-2.1build1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1build4 libxcb-render0_1.14-3ubuntu2 libxcb-shm0_1.14-3ubuntu2 libxcb1_1.14-3ubuntu2 libxdmcp6_1:1.1.3-0ubuntu4 libxext6_2:1.3.4-0ubuntu4 libxft2_2.3.3-0ubuntu4 libxml2_2.9.12+dfsg-5 libxrender1_1:0.9.10-1build3 libxss1_1:1.2.3-1build1 libxt6_1:1.2.0-1build1 libxxhash0_0.8.0-2build1 libyaml-0-2_0.2.2-1build1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.13.0-19.19 lockfile-progs_0.1.19 login_1:4.8.1-1ubuntu9 logsave_1.46.3-1ubuntu3 lsb-base_11.1.0ubuntu3 lto-disabled-list_16 m4_1.4.18-5ubuntu1 mailcap_3.70ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-2build1 mawk_1.3.4.20200120-2build1 media-types_4.0.0 mime-support_3.66 mount_2.36.1-8ubuntu2 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 openssl_1.1.1l-1ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 poppler-utils_21.06.1-1 procps_2:3.3.17-5ubuntu3 python-matplotlib-data_3.3.4-2 python3_3.9.4-1ubuntu2 python3-all_3.9.4-1ubuntu2 python3-biopython_1.78+dfsg-5ubuntu1 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-0ubuntu1 python3-distutils_3.9.7-1 python3-future_0.18.2-5 python3-joblib_0.17.0-4 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.9.7-1 python3-matplotlib_3.3.4-2 python3-minimal_3.9.4-1ubuntu2 python3-networkx_2.4-4ubuntu1 python3-numpy_1:1.20.2-1ubuntu1 python3-pandas_1.1.5+dfsg-2 python3-pandas-lib_1.1.5+dfsg-2 python3-pil_8.3.2-1 python3-pkg-resources_58.2.0-1 python3-pomegranate_0.13.5-1 python3-pyfaidx_0.6.2-1 python3-pyparsing_2.4.7-1 python3-pysam_0.17.0+ds-2 python3-renderpm_3.6.1-1 python3-reportlab_3.6.1-1 python3-reportlab-accel_3.6.1-1 python3-scipy_1.6.0-2 python3-setuptools_58.2.0-1 python3-six_1.16.0-2 python3-tz_2021.3-1 python3-vcf_0.6.8+git20170215.476169c-8 python3-yaml_5.4.1-1 python3.10_3.10.0-3 python3.10-minimal_3.10.0-3 python3.9_3.9.7-4 python3.9-minimal_3.9.7-4 r-base-core_4.1.1-2 r-bioc-biocgenerics_0.38.0-1 r-bioc-dnacopy_1.66.0-1 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-cnvkit-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.17 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 ttf-bitstream-vera_1.10-8.1 tzdata_2021a-2ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unzip_6.0-26ubuntu2 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu2 x11-common_1:7.7+23ubuntu1 xdg-utils_1.1.3-2ubuntu2 xz-utils_5.2.5-2build1 zip_3.0-12build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Oct 15 06:51:53 2021 UTC gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.9-2.dsc dpkg-source: info: extracting cnvkit in /<> dpkg-source: info: unpacking cnvkit_0.9.9.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.9-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-py-ext dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22292071 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22292071 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22292071 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.9-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/<>/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn 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 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 all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/<>/test' if [ -f cnvkit ]; then mv cnvkit cnvkit.py; fi dh_auto_clean I: pybuild base:232: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.10_cnvkit/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:232: python3.9 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running clean removing '/<>/.pybuild/cpython3_3.9_cnvkit/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf test/p2-20-metrics.tsv test/p2-5_5-metrics.tsv test/p2-9_2-metrics.tsv rm -rf test/build CNVkit.egg-info make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:232: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running config I: pybuild base:232: python3.9 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted build if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_build I: pybuild base:232: /usr/bin/python3.10 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running build running build_py creating /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/target.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/core.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/params.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/rna.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/importers.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/call.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/plots.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/batch.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/vary.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/reference.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/export.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/fix.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/access.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/commands.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/reports.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/_version.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib creating /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation creating /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/gary.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/combiners.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/subdivide.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/intersect.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/subtract.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/merge.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/chromsort.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/__init__.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome creating /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.10 copying and adjusting /<>/cnvkit -> build/scripts-3.10 copying /<>/scripts/snpfilter.sh -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-cnv_annotate -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-guess_baits -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-cnv_updater -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-genome_instability_index -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-reference2targets -> build/scripts-3.10 copying and adjusting /<>/scripts/cnvkit-skg_convert -> build/scripts-3.10 changing mode of build/scripts-3.10/cnvkit from 644 to 755 changing mode of build/scripts-3.10/cnvkit-cnv_annotate from 644 to 755 changing mode of build/scripts-3.10/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.10/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.10/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.10/cnvkit-genome_instability_index from 644 to 755 changing mode of build/scripts-3.10/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.10/cnvkit-skg_convert from 644 to 755 I: pybuild base:232: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running build running build_py creating /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/target.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/core.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/params.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/rna.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/importers.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/call.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/plots.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/bintest.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/batch.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/cluster.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/vary.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reference.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/export.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/fix.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/access.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/commands.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/reports.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/_version.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib creating /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation creating /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/gary.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/combiners.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subdivide.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/intersect.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/subtract.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/merge.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/chromsort.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/__init__.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome creating /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio running build_scripts creating build/scripts-3.9 copying and adjusting /<>/cnvkit -> build/scripts-3.9 copying /<>/scripts/snpfilter.sh -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-cnv_annotate -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-guess_baits -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-cnv_updater -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-genome_instability_index -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-reference2targets -> build/scripts-3.9 copying and adjusting /<>/scripts/cnvkit-skg_convert -> build/scripts-3.9 changing mode of build/scripts-3.9/cnvkit from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_annotate from 644 to 755 changing mode of build/scripts-3.9/cnvkit-guess_baits from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_updater from 644 to 755 changing mode of build/scripts-3.9/cnvkit-cnv_expression_correlate from 644 to 755 changing mode of build/scripts-3.9/cnvkit-genome_instability_index from 644 to 755 changing mode of build/scripts-3.9/cnvkit-reference2targets from 644 to 755 changing mode of build/scripts-3.9/cnvkit-skg_convert from 644 to 755 cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd test && /usr/bin/make make[2]: Entering directory '/<>/test' python3 ../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/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dq9w08tf because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Created directory build/ Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rlchqfpc because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 338 (5.0858%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 " chr1:2435319-2436685 log2=-0.709 spread=0.503 ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 " chr1:120611883-120612051 log2=0.070 spread=0.050 NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 " chr1:156842391-156842479 log2=-0.398 spread=0.290 MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 " chr1:183481886-183481951 log2=-0.040 spread=0.119 CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 " chr1:243800859-243801066 log2=0.023 spread=0.063 MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 " chr2:25536716-25536891 log2=0.702 spread=0.033 MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 REL chr2:61108881-61109061 log2=1.026 spread=0.559 " chr2:61128072-61128256 log2=0.115 spread=0.173 " chr2:61145275-61145462 log2=0.014 spread=0.099 CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 " chr2:128095237-128095425 log2=0.215 spread=0.212 METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 " chr3:97160189-97160367 log2=-0.050 spread=0.191 ATR chr3:142254935-142255077 log2=0.024 spread=0.027 " chr3:142286854-142287031 log2=-0.076 spread=0.116 GAK chr4:896278-896357 log2=-1.505 spread=1.261 FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 " chr4:1803044-1803507 log2=-0.073 spread=0.117 " chr4:1808792-1809022 log2=0.252 spread=0.108 CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 " chr4:178514600-178514725 log2=-0.098 spread=0.096 TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 " chr5:1295312-1295381 log2=-0.690 spread=0.462 CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 " chr5:25519857-25520034 log2=-0.015 spread=0.095 RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 " chr5:38962338-38962525 log2=0.005 spread=0.019 " chr5:38966685-38966862 log2=0.006 spread=0.165 " chr5:38978620-38978763 log2=0.040 spread=0.030 " chr5:39074133-39074327 log2=-0.158 spread=0.139 CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 " chr5:51030131-51030313 log2=-0.034 spread=0.192 MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 " chr5:56168412-56168590 log2=0.479 spread=0.038 CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 " chr5:86637023-86637168 log2=0.054 spread=0.111 " chr5:86642414-86642592 log2=0.254 spread=0.162 " chr5:86648912-86649096 log2=0.092 spread=0.062 " chr5:86670598-86670778 log2=0.222 spread=0.198 MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 APC chr5:112101965-112102138 log2=0.104 spread=0.217 NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 " chr5:170837567-170837631 log2=0.085 spread=0.349 FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 " chr5:180046203-180046404 log2=-1.531 spread=0.722 " chr5:180076418-180076603 log2=-2.224 spread=1.416 TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 " chr6:31939599-31940313 log2=-19.582 spread=0.181 STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 " chr6:31946632-31946824 log2=-20.052 spread=0.088 " chr6:31947142-31947366 log2=-20.114 spread=0.066 " chr6:31948176-31948360 log2=-19.982 spread=0.149 " chr6:31948382-31948612 log2=-19.757 spread=0.165 " chr6:31948730-31949253 log2=-20.048 spread=0.014 NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 " chr6:32164046-32164227 log2=-19.755 spread=0.189 " chr6:32164652-32164888 log2=-19.984 spread=0.154 " chr6:32165021-32165403 log2=-19.625 spread=0.196 " chr6:32166163-32166545 log2=-20.043 spread=0.072 " chr6:32166648-32166962 log2=-3.514 spread=5.742 " chr6:32168554-32168821 log2=-19.601 spread=0.197 " chr6:32168844-32169306 log2=-19.683 spread=0.166 " chr6:32169801-32170391 log2=-19.405 spread=0.205 " chr6:32171492-32171691 log2=-20.095 spread=0.101 " chr6:32171861-32172198 log2=-3.141 spread=7.288 " chr6:32178478-32178749 log2=-19.927 spread=0.164 " chr6:32180197-32180441 log2=-10.902 spread=9.532 " chr6:32180544-32180722 log2=-19.675 spread=0.186 " chr6:32180857-32181062 log2=-19.562 spread=0.227 " chr6:32181411-32181646 log2=-19.966 spread=0.171 " chr6:32181832-32182066 log2=-19.961 spread=0.172 " chr6:32182948-32183194 log2=-19.935 spread=0.168 " chr6:32184667-32185079 log2=-19.923 spread=0.165 " chr6:32185720-32185919 log2=-19.707 spread=0.197 " chr6:32187317-32187601 log2=-19.765 spread=0.173 " chr6:32187871-32188094 log2=-19.660 spread=0.188 " chr6:32188127-32188451 log2=-19.622 spread=0.169 " chr6:32188481-32188693 log2=-19.902 spread=0.132 " chr6:32188704-32189133 log2=-19.501 spread=0.193 " chr6:32190258-32190616 log2=-19.570 spread=0.209 " chr6:32190724-32190908 log2=-19.540 spread=0.232 " chr6:32191570-32191668 log2=-19.773 spread=0.178 " chr6:32191676-32191753 log2=-19.374 spread=0.201 FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 " chr6:128316545-128316699 log2=-0.070 spread=0.050 MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 " chr6:157099442-157099991 log2=-0.846 spread=0.504 " chr6:157100042-157100634 log2=-1.570 spread=0.825 IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 " chr7:98491365-98491541 log2=0.209 spread=0.153 " chr7:98493314-98493496 log2=0.389 spread=0.207 SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 " chr7:128829048-128829358 log2=-0.474 spread=0.315 BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 " chr7:140484736-140484912 log2=0.081 spread=0.150 " chr7:140487956-140488430 log2=-0.089 spread=0.142 " chr7:140493336-140493442 log2=-0.340 spread=0.283 " chr7:140624315-140624540 log2=-0.497 spread=0.342 TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 WRN chr8:30925752-30925890 log2=0.120 spread=0.158 " chr8:30941153-30941335 log2=0.079 spread=0.294 " chr8:30942625-30942802 log2=0.044 spread=0.247 " chr8:30947918-30948092 log2=0.151 spread=0.124 " chr8:31000128-31000252 log2=-0.099 spread=0.098 " chr8:31001006-31001182 log2=-0.002 spread=0.062 GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 " chr8:37698557-37699898 log2=-0.612 spread=0.029 ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 " chr8:48845528-48845758 log2=0.056 spread=0.196 " chr8:48866846-48867043 log2=-0.067 spread=0.097 " chr8:48868369-48868526 log2=-0.239 spread=0.174 " chr8:48872485-48872722 log2=-0.636 spread=0.464 CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 " chr9:2101491-2101640 log2=0.244 spread=0.104 JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 " chr9:5067014-5067883 log2=0.146 spread=0.089 " chr9:5068184-5070306 log2=0.133 spread=0.092 " chr9:5076944-5077152 log2=0.046 spread=0.137 PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 " chr9:21986759-21986899 log2=0.058 spread=0.175 LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 " chr9:87425375-87425452 log2=0.494 spread=0.066 PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 " chr9:139250747-139251032 log2=-0.223 spread=0.273 " chr9:139252418-139252703 log2=-0.512 spread=0.264 NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 " chr9:139417262-139417677 log2=-0.173 spread=0.191 " chr9:139440110-139440287 log2=-1.257 spread=0.500 MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 CGH chr10:22505654-22505837 log2=0.072 spread=0.107 RET chr10:43572644-43572830 log2=-1.376 spread=1.092 " chr10:43600360-43600677 log2=-0.341 spread=0.222 PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 " chr10:89685254-89685374 log2=0.244 spread=0.259 TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 " chr10:93579008-93579121 log2=0.166 spread=0.220 SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 " chr10:112679716-112679934 log2=-0.008 spread=0.028 CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 " chr11:94170270-94170454 log2=0.095 spread=0.285 YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 ATM chr11:108153392-108153639 log2=0.113 spread=0.136 " chr11:108164020-108164234 log2=-0.056 spread=0.040 " chr11:108217986-108218135 log2=0.359 spread=0.277 MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 " chr12:25391004-25391186 log2=0.368 spread=0.128 DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 " chr12:51206782-51207287 log2=-0.012 spread=0.101 PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 " chr13:26970356-26970536 log2=0.137 spread=0.121 FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 " chr13:32903506-32903689 log2=0.019 spread=0.232 " chr13:32918645-32918823 log2=0.158 spread=0.114 " chr13:32920899-32921077 log2=0.014 spread=0.247 RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 " chr13:48919164-48919369 log2=0.025 spread=0.094 " chr13:48921877-48922044 log2=0.106 spread=0.147 " chr13:48923026-48923204 log2=0.360 spread=0.016 " chr13:48938965-48939147 log2=0.084 spread=0.356 " chr13:48941578-48941767 log2=0.238 spread=0.212 " chr13:48947486-48947665 log2=0.025 spread=0.126 " chr13:48954166-48954251 log2=0.061 spread=0.273 " chr13:49037815-49038005 log2=0.063 spread=0.062 " chr13:49047410-49047589 log2=0.053 spread=0.170 CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 " chr13:85527771-85527948 log2=0.007 spread=0.222 GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 " chr13:110438332-110438432 log2=-3.643 spread=2.325 CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 " chr14:20291466-20291612 log2=0.697 spread=0.248 NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 " chr14:36989195-36989373 log2=0.023 spread=0.162 SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 " chr14:50619741-50619923 log2=0.003 spread=0.272 " chr14:50697856-50698044 log2=0.277 spread=0.334 MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 " chr14:71275790-71275923 log2=-2.815 spread=1.938 TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 CGH chr15:20870700-20870881 log2=1.102 spread=0.611 " chr15:38544477-38545455 log2=-0.348 spread=0.179 SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 " chr15:41803968-41804185 log2=-2.202 spread=0.188 " chr15:41804261-41804494 log2=-0.402 spread=0.392 NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 " chr16:2611404-2611585 log2=-5.171 spread=1.963 " chr16:2611721-2611943 log2=-11.810 spread=9.172 " chr16:2615504-2615725 log2=-20.113 spread=0.007 " chr16:2616307-2616486 log2=-20.054 spread=0.072 " chr16:2631267-2631414 log2=-20.009 spread=0.061 " chr16:2631583-2631734 log2=-20.089 spread=0.090 " chr16:2633363-2633616 log2=-20.101 spread=0.089 CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 CGH chr16:31526705-31526886 log2=0.057 spread=0.074 CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 " chr16:50826460-50826650 log2=0.239 spread=0.204 CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 " chr16:60005694-60005857 log2=-0.366 spread=0.298 CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 " chr17:12011053-12011253 log2=0.028 spread=0.232 NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 " chr17:29496854-29497046 log2=0.226 spread=0.193 RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 " chr17:30519172-30519355 log2=0.163 spread=0.289 " chr17:30525911-30526093 log2=-0.157 spread=0.046 ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 " chr19:2210351-2210545 log2=-0.860 spread=0.261 " chr19:2226130-2227152 log2=-0.113 spread=0.120 GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 " chr19:15311544-15311749 log2=-1.887 spread=1.202 JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 " chr19:33792774-33793010 log2=-1.781 spread=0.127 " chr19:33793014-33793356 log2=-0.541 spread=0.385 CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 " chr19:45873698-45873881 log2=-0.522 spread=0.327 BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 " chr21:36265140-36265318 log2=0.042 spread=0.039 CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 " chr22:29115325-29115465 log2=0.055 spread=0.390 SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 " chrX:1317372-1317594 log2=-21.121 spread=0.049 " chrX:1321225-1321435 log2=-20.851 spread=0.196 " chrX:1325274-1325530 log2=-21.121 spread=0.011 " chrX:1327651-1327830 log2=-21.000 spread=0.029 " chrX:1331391-1331576 log2=-21.018 spread=0.052 KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 " chrX:123185143-123185290 log2=-1.018 spread=0.062 " chrX:123202378-123202544 log2=-0.959 spread=0.103 FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 " chrY:9008607-9008759 log2=-1.012 spread=0.097 " chrY:13131970-13132039 log2=-1.004 spread=0.074 " chrY:19506485-19506650 log2=-1.018 spread=0.034 " chrY:21033918-21034071 log2=-1.013 spread=0.057 " chrY:28463435-28463622 log2=-0.952 spread=0.039 " chrY:28514033-28514208 log2=-0.992 spread=0.026 Antitargets: 108 (0.8597%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-m8ujj6mp because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-5_5 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-5_5 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.14 x more variable than antitargets Wrote build/p2-5_5.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dwzadbn4 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-6i29cc16 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5culuui3 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-9_2 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-9_2 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.75 x more variable than antitargets Wrote build/p2-9_2.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-__pb7l9u because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-1x754bvr because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-43vgd2f9 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_1 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_1 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.14 x more variable than antitargets Wrote build/p2-20_1.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5gt0os03 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-vwdox571 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-3rkajlzs because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_2 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_2 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.09 x more variable than antitargets Wrote build/p2-20_2.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h0osuvm8 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2wd4n8gh because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-foh3xn3r because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_3 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_3 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Antitargets are 1.08 x more variable than targets Wrote build/p2-20_3.cnr with 18763 regions python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dkkfo5g4 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ciznsxdp because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0mbib7ek because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_4 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_4 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.43 x more variable than antitargets Wrote build/p2-20_4.cnr with 18763 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lgia62jf because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Processing target: p2-20_5 Keeping 6308 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_5 Keeping 12455 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 2.60 x more variable than antitargets Wrote build/p2-20_5.cnr with 18763 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-n_7_dfk_ because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-5_5.cns with 71 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4fmd1ccv because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 1 / 949 bins on chromosome chr6 Dropped 27 / 49 bins on chromosome chrY Wrote build/p2-9_2.cns with 107 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-v9_pgwce because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY Wrote build/p2-20_1.cns with 117 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-z0wwyh4p because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 7 / 49 bins on chromosome chrY Wrote build/p2-20_2.cns with 125 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5nkjjvwv because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 11 / 49 bins on chromosome chrY Wrote build/p2-20_3.cns with 74 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ru4mxw9d because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 8 / 49 bins on chromosome chrY Wrote build/p2-20_4.cns with 137 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tht2z3ov because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 6 / 49 bins on chromosome chrY Wrote build/p2-20_5.cns with 129 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lcta9bvt because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-5_5-scatter.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-u7998a71 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Smoothing overshot at 3 / 97 indices: (-19.887157566382907, -3.337830278732162) vs. original (-19.2826, -0.27873000000000003) Wrote p2-9_2-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-r6z29gp6 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 1480 probes and 0 selected genes in region chr1 Wrote p2-9_2-chr1-scatter.pdf python3 ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-o_3u0i31 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 201 probes and 0 selected genes in region chr21 Wrote p2-9_2-chr21-scatter.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-rjfq4t39 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 330 probes and 13 selected genes in region chr9:149999-45000000 Wrote p2-9_2-chr9p-scatter.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-25piek77 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Showing 179 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wvo4izof because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Detected file format: bed Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 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 /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/pdfunite python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-aowkacau because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-pee_5naj because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-t9rg2agn because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-fhta6ch5 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-jds0ghdj because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Wrote p2-5_5-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wzvn5l3r because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Wrote p2-9_2-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-i_cp21kx because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Wrote p2-20_1-cbs-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf Matplotlib created a temporary config/cache directory at /tmp/matplotlib-njaog7um because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Wrote p2-20_2-cbs-diagram.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-xayd9z4p because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Wrote p2-5_5-both-diagram.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ohgio8yi because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Wrote p2-9_2-both-diagram.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d4lq4lp6 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Wrote p2-20_1-both-diagram.pdf python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-me580twe because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Wrote p2-20_2-both-diagram.pdf 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 /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/pdfunite python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-onn0wibu because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Treating sample p2-9_2 as female Treating sample p2-20_1 as female Treating sample p2-20_2 as female Treating sample p2-20_3 as female Treating sample p2-20_4 as female Treating sample p2-20_5 as female Wrote heatmap-picard.pdf python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-00r61uma because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Found 15 gene breakpoints Wrote p2-9_2-breaks.txt python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-j8rv_zm8 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Found 345 gene-level gains and losses Wrote p2-9_2-genemetrics.txt python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lcjbyxm6 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote gender-picard.txt python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tvd21sdk because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-all.cdt python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-bvxaye4d because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-all-jtv.txt python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-s0viov93 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-all.seg python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5q5ed2f9 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2.nexus python3 ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Matplotlib created a temporary config/cache directory at /tmp/matplotlib-9moahif5 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Placed 705 variants into 18763 bins Wrote p2-9_2.nexus-ogt python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d9vqdm4j because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 71 regions python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-w08s2xgx because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 107 regions python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k1uw2_tv because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_1 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 117 regions python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-d18m70mn because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_2 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 125 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-k6wx60x6 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_3 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 74 regions python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-lhfceju4 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_4 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 137 regions python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Matplotlib created a temporary config/cache directory at /tmp/matplotlib-tmfr_sbk because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-20_5 as female Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 129 regions python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-gqa1uodv because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-5_5.call as female Treating sample p2-9_2.call as female Treating sample p2-20_1.call as female Treating sample p2-20_2.call as female Treating sample p2-20_3.call as female Treating sample p2-20_4.call as female Treating sample p2-20_5.call as female Wrote p2-all.bed python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-h4ma8grn because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Treating sample p2-9_2.call as female Wrote p2-9_2.vcf python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Matplotlib created a temporary config/cache directory at /tmp/matplotlib-wqup9129 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2.theta2.input python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode --t-test \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem --smooth-bootstrap Matplotlib created a temporary config/cache directory at /tmp/matplotlib-p3l8kef5 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2-segmetrics.cns with 107 regions python3 ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ --ci -b 50 -a 0.5 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-ad7ul84g because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-5_5-segmetrics.cns with 71 regions python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-x00qsn2o because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-5_5-metrics.tsv python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Matplotlib created a temporary config/cache directory at /tmp/matplotlib-2x3qkv34 because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-9_2-metrics.tsv python3 ../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 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-4mkmel3g because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. Wrote p2-20-metrics.tsv make[2]: Leaving directory '/<>/test' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/<>/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn 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 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 all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/<>/test' rm -Rf test/build test/*.tsv make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/<>' [ -f cnvkit.py ] && mv cnvkit.py cnvkit || true # may not exist after interrupted install if [ -f scripts/cnv_annotate.py ]; then \ cd scripts && for script in *.py; do \ mv ${script} cnvkit-${script%%.py}; \ done; \ fi dh_auto_install I: pybuild base:232: /usr/bin/python3.10 setup.py install --root /<>/debian/cnvkit /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running install running build running build_py running build_scripts running install_lib creating /<>/debian/cnvkit/usr creating /<>/debian/cnvkit/usr/lib creating /<>/debian/cnvkit/usr/lib/python3.10 creating /<>/debian/cnvkit/usr/lib/python3.10/dist-packages creating /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/diagram.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/target.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/coverage.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/metrics.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/smoothing.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/core.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/params.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/cnary.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/descriptives.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/import_rna.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/rna.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/importers.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/call.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/heatmap.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/samutil.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/autobin.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/plots.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/scatter.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/bintest.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/cmdutil.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/batch.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segfilters.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/cluster.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/vary.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/reference.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/parallel.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/export.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/fix.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/access.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/commands.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/reports.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/_version.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmetrics.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/antitarget.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/haar.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/flasso.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/none.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/cbs.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.10_cnvkit/build/cnvlib/segmentation/hmm.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation creating /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/gary.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/combiners.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome creating /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/seg.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/picard.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/seqdict.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/vcfsimple.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/gff.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/genepred.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/tab.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/vcfio.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/bedio.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/util.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/tabio/textcoord.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/subdivide.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/intersect.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/subtract.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/merge.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/chromsort.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.10_cnvkit/build/skgenome/rangelabel.py -> /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/diagram.py to diagram.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/target.py to target.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/coverage.py to coverage.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/metrics.py to metrics.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/smoothing.py to smoothing.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/core.py to core.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/params.py to params.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/cnary.py to cnary.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/descriptives.py to descriptives.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/import_rna.py to import_rna.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/rna.py to rna.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/importers.py to importers.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/call.py to call.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/heatmap.py to heatmap.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/samutil.py to samutil.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/autobin.py to autobin.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/plots.py to plots.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/scatter.py to scatter.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/bintest.py to bintest.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/batch.py to batch.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segfilters.py to segfilters.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/cluster.py to cluster.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/vary.py to vary.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/reference.py to reference.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/parallel.py to parallel.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/export.py to export.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/fix.py to fix.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/access.py to access.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/commands.py to commands.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/reports.py to reports.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/_version.py to _version.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/antitarget.py to antitarget.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/none.py to none.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/gary.py to gary.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/combiners.py to combiners.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/seg.py to seg.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/picard.py to picard.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/gff.py to gff.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/tab.py to tab.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/util.py to util.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/subdivide.py to subdivide.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/intersect.py to intersect.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/subtract.py to subtract.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/merge.py to merge.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/chromsort.py to chromsort.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-310.pyc running install_egg_info running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /<>/debian/cnvkit/usr/lib/python3.10/dist-packages/CNVkit-0.9.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/snpfilter.sh -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-cnv_annotate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-guess_baits -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-cnv_updater -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-cnv_expression_correlate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-genome_instability_index -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-reference2targets -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.10/cnvkit-skg_convert -> /<>/debian/cnvkit/usr/bin changing mode of /<>/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-genome_instability_index to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 I: pybuild base:232: /usr/bin/python3 setup.py install --root /<>/debian/cnvkit /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'build-lib' will not be supported in future versions. Please use the underscore name 'build_lib' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-layout' will not be supported in future versions. Please use the underscore name 'install_layout' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-scripts' will not be supported in future versions. Please use the underscore name 'install_scripts' instead warnings.warn( /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'install-lib' will not be supported in future versions. Please use the underscore name 'install_lib' instead warnings.warn( running install running build running build_py running build_scripts running install_lib creating /<>/debian/cnvkit/usr/lib/python3.9 creating /<>/debian/cnvkit/usr/lib/python3.9/dist-packages creating /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/diagram.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/target.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/coverage.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/metrics.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/smoothing.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/core.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/params.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cnary.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/descriptives.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/import_rna.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/rna.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/importers.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/call.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/heatmap.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/samutil.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/autobin.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/plots.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/scatter.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/bintest.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cmdutil.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/batch.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segfilters.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/cluster.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/vary.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reference.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/parallel.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/export.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/fix.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/access.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/commands.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/reports.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/_version.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmetrics.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/antitarget.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/haar.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/flasso.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/none.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/cbs.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.9_cnvkit/build/cnvlib/segmentation/hmm.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation creating /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/gary.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/combiners.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome creating /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seg.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/picard.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/seqdict.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfsimple.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/gff.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/genepred.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/tab.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/vcfio.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/bedio.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/util.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/tabio/textcoord.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subdivide.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/intersect.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/subtract.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/merge.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/chromsort.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.9_cnvkit/build/skgenome/rangelabel.py -> /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/diagram.py to diagram.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/target.py to target.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/coverage.py to coverage.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/metrics.py to metrics.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/smoothing.py to smoothing.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/core.py to core.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/params.py to params.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cnary.py to cnary.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/descriptives.py to descriptives.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/import_rna.py to import_rna.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/rna.py to rna.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/importers.py to importers.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/call.py to call.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/heatmap.py to heatmap.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/samutil.py to samutil.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/autobin.py to autobin.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/plots.py to plots.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/scatter.py to scatter.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/bintest.py to bintest.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/batch.py to batch.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segfilters.py to segfilters.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/cluster.py to cluster.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/vary.py to vary.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reference.py to reference.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/parallel.py to parallel.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/__init__.py to __init__.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/export.py to export.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/fix.py to fix.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/access.py to access.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/commands.py to commands.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/reports.py to reports.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/_version.py to _version.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/antitarget.py to antitarget.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/none.py to none.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/gary.py to gary.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/combiners.py to combiners.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seg.py to seg.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/picard.py to picard.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/gff.py to gff.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/tab.py to tab.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/util.py to util.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subdivide.py to subdivide.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/intersect.py to intersect.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/subtract.py to subtract.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/merge.py to merge.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/chromsort.py to chromsort.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/__init__.py to __init__.cpython-39.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-39.pyc running install_egg_info running egg_info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt reading manifest file 'CNVkit.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /<>/debian/cnvkit/usr/lib/python3.9/dist-packages/CNVkit-0.9.9.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.9/snpfilter.sh -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_annotate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-guess_baits -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_updater -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-cnv_expression_correlate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-genome_instability_index -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-reference2targets -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.9/cnvkit-skg_convert -> /<>/debian/cnvkit/usr/bin changing mode of /<>/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-guess_baits to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-genome_instability_index to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-reference2targets to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-skg_convert to 755 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.9 Matplotlib created a temporary config/cache directory at /tmp/matplotlib-serzmb8z because the default path (/sbuild-nonexistent/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.9 --help-option='-h' \ ./cnvkit-reference2targets --name='Extract target and antitarget BED files from a CNVkit reference file.' \ > ../debian/cnvkit-reference2targets.1; cd scripts && for script in cnvkit-*; do \ mv ${script} ${script##cnvkit-}.py; \ done mv cnvkit cnvkit.py make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installexamples -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild dh_shlibdeps -a -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. INFO: pkgstriptranslations version 148 pkgstriptranslations: processing cnvkit (in debian/cnvkit); do_strip: , oemstrip: /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgstripfiles: processing control file: debian/cnvkit/DEBIAN/control, package cnvkit, directory debian/cnvkit pkgstripfiles: Truncating usr/share/doc/cnvkit/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package cnvkit ... pkgstripfiles: No PNG files. dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.9-2_arm64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../cnvkit_0.9.9-2_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2021-10-22T12:10:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cnvkit_0.9.9-2_arm64.changes: ----------------------------- Format: 1.8 Date: Fri, 15 Oct 2021 12:11:06 +0530 Source: cnvkit Binary: cnvkit Built-For-Profiles: noudeb Architecture: arm64 Version: 0.9.9-2 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: cnvkit - Copy number variant detection from targeted DNA sequencing Changes: cnvkit (0.9.9-2) unstable; urgency=medium . * Team Upload. * Re-diff patches (refresh) * d/rules: do not run tests in parallel Checksums-Sha1: cd9ce7f9fff0ac9ad9ccb22a98c0d7dac7d4b813 10252 cnvkit_0.9.9-2_arm64.buildinfo 7be0701256573605604c05191a7ca0a487ac87c6 16135876 cnvkit_0.9.9-2_arm64.deb Checksums-Sha256: d0335a37727baed384478475bfe55c6ff9d96ed229e63271c2d5d33158886131 10252 cnvkit_0.9.9-2_arm64.buildinfo da2bfb1ca61ac5e471135c9d02838d6f6fa486e5d115b358e52f163b2f6defa1 16135876 cnvkit_0.9.9-2_arm64.deb Files: 4611435eed9d0fe0477a2df82a9f7908 10252 science optional cnvkit_0.9.9-2_arm64.buildinfo 0fc0dba337a6c860aa119c00754ce085 16135876 science optional cnvkit_0.9.9-2_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: cnvkit Binary: cnvkit Architecture: arm64 Version: 0.9.9-2 Checksums-Md5: 0fc0dba337a6c860aa119c00754ce085 16135876 cnvkit_0.9.9-2_arm64.deb Checksums-Sha1: 7be0701256573605604c05191a7ca0a487ac87c6 16135876 cnvkit_0.9.9-2_arm64.deb Checksums-Sha256: da2bfb1ca61ac5e471135c9d02838d6f6fa486e5d115b358e52f163b2f6defa1 16135876 cnvkit_0.9.9-2_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Fri, 22 Oct 2021 12:10:20 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.4-2), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu1), base-passwd (= 3.5.52), bash (= 5.1-3ubuntu2), binutils (= 2.37-7ubuntu1), binutils-aarch64-linux-gnu (= 2.37-7ubuntu1), binutils-common (= 2.37-7ubuntu1), bsdextrautils (= 2.36.1-8ubuntu2), bsdutils (= 1:2.36.1-8ubuntu2), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-4ubuntu4), ca-certificates (= 20211016), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-10ubuntu1), dash (= 0.5.11+git20210120+802ebd4-1build1), debconf (= 1.5.77), debhelper (= 13.3.4ubuntu2), debianutils (= 5.5-1), debugedit (= 1:5.0-0ubuntu2), dh-autoreconf (= 20), dh-python (= 5.20211021), dh-strip-nondeterminism (= 1.12.0-2), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu2), dpkg-dev (= 1.20.9ubuntu2), dwz (= 0.14-1build1), file (= 1:5.39-3build1), findutils (= 4.8.0-1ubuntu2), fontconfig (= 2.13.1-4.2ubuntu4), fontconfig-config (= 2.13.1-4.2ubuntu4), fonts-lyx (= 2.3.6-1), fonts-urw-base35 (= 20200910-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-10ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-10ubuntu1), gcc-11-base (= 11.2.0-10ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-0ubuntu1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), help2man (= 1.48.5), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-10ubuntu1), libatomic1 (= 11.2.0-10ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-7ubuntu1), libblas3 (= 3.9.0-3ubuntu3), libblkid1 (= 2.36.1-8ubuntu2), libbrotli1 (= 1.0.9-2build4), libbsd0 (= 0.11.3-1ubuntu3), libbz2-1.0 (= 1.0.8-4ubuntu4), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcairo2 (= 1.16.0-5ubuntu2), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-10ubuntu1), libcom-err2 (= 1.46.3-1ubuntu3), libcrypt-dev (= 1:4.4.18-4ubuntu2), libcrypt1 (= 1:4.4.18-4ubuntu2), libctf-nobfd0 (= 2.37-7ubuntu1), libctf0 (= 2.37-7ubuntu1), libcurl3-gnutls (= 7.74.0-1.3ubuntu2), libcurl4 (= 7.74.0-1.3ubuntu2), libdatrie1 (= 0.2.13-1ubuntu3), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.3.4ubuntu2), libdeflate0 (= 1.7-2ubuntu2), libdpkg-perl (= 1.20.9ubuntu2), libdw1 (= 0.185-2), libedit2 (= 3.1-20210910-1), libelf1 (= 0.185-2), libexpat1 (= 2.4.1-2), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.0-2), libfontconfig1 (= 2.13.1-4.2ubuntu4), libfreetype6 (= 2.11.0+dfsg-1), libfribidi0 (= 1.0.8-2ubuntu2), libgcc-11-dev (= 11.2.0-10ubuntu1), libgcc-s1 (= 11.2.0-10ubuntu1), libgcrypt20 (= 1.8.7-5ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgfortran5 (= 11.2.0-10ubuntu1), libglib2.0-0 (= 2.68.4-1ubuntu1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.1-5ubuntu1), libgomp1 (= 11.2.0-10ubuntu1), libgpg-error0 (= 1.42-3), libgraphite2-3 (= 1.3.14-1build1), libgssapi-krb5-2 (= 1.18.3-7), libharfbuzz0b (= 2.7.4-1ubuntu2), libhogweed6 (= 3.7.3-1build1), libhts3 (= 1.13+ds-2), libhtscodecs2 (= 1.1.1-3), libhwasan0 (= 11.2.0-10ubuntu1), libice6 (= 2:1.0.10-1build1), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libimagequant0 (= 2.12.2-1.1build1), libisl23 (= 0.24-2), libitm1 (= 11.2.0-10ubuntu1), libjbig0 (= 2.1-3.1build2), libjpeg-turbo8 (= 2.0.6-0ubuntu3), libjpeg8 (= 8c-2ubuntu8), libjs-jquery (= 3.5.1+dfsg+~3.5.5-7), libjs-jquery-ui (= 1.12.1+dfsg-8), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblapack3 (= 3.9.0-3ubuntu3), liblbfgsb0 (= 3.0+dfsg.3-9), liblcms2-2 (= 2.12~rc1-2build1), libldap-2.5-0 (= 2.5.6+dfsg-1~exp1ubuntu1), liblocale-gettext-perl (= 1.07-4build2), liblsan0 (= 11.2.0-10ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.39-3build1), libmagic1 (= 1:5.39-3build1), libmd0 (= 1.0.4-1), libmount1 (= 2.36.1-8ubuntu2), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libncurses6 (= 6.2+20210905-1), libncursesw6 (= 6.2+20210905-1), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libnspr4 (= 2:4.32-1), libnss3 (= 2:3.68-1ubuntu1), libopenjp2-7 (= 2.4.0-3), libp11-kit0 (= 0.24.0-5), libpam-modules (= 1.3.1-5ubuntu11), libpam-modules-bin (= 1.3.1-5ubuntu11), libpam-runtime (= 1.3.1-5ubuntu11), libpam0g (= 1.3.1-5ubuntu11), libpango-1.0-0 (= 1.48.10+ds1-1), libpangocairo-1.0-0 (= 1.48.10+ds1-1), libpangoft2-1.0-0 (= 1.48.10+ds1-1), libpaper-utils (= 1.1.28build1), libpaper1 (= 1.1.28build1), libpcre2-8-0 (= 10.37-0ubuntu2), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.3-1build1), libpixman-1-0 (= 0.40.0-1build3), libpng16-16 (= 1.6.37-3build4), libpoppler111 (= 21.06.1-1), libprocps8 (= 2:3.3.17-5ubuntu3), libpsl5 (= 0.21.0-1.2build1), libpython3-stdlib (= 3.9.4-1ubuntu2), libpython3.10-minimal (= 3.10.0-3), libpython3.10-stdlib (= 3.10.0-3), libpython3.9-minimal (= 3.9.7-4), libpython3.9-stdlib (= 3.9.7-4), libraqm0 (= 0.7.0-4), libreadline8 (= 8.1-2build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libsasl2-2 (= 2.1.27+dfsg-2.1build1), libsasl2-modules-db (= 2.1.27+dfsg-2.1build1), libseccomp2 (= 2.5.1-1ubuntu2), libselinux1 (= 3.1-3build3), libsigsegv2 (= 2.13-1ubuntu2), libsm6 (= 2:1.2.3-1build1), libsmartcols1 (= 2.36.1-8ubuntu2), libsqlite3-0 (= 3.36.0-2), libssh-4 (= 0.9.6-1), libssl1.1 (= 1.1.1l-1ubuntu1), libstdc++-11-dev (= 11.2.0-10ubuntu1), libstdc++6 (= 11.2.0-10ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 248.3-1ubuntu8), libtasn1-6 (= 4.17.0-2), libtcl8.6 (= 8.6.11+dfsg-1build1), libthai-data (= 0.1.28-4.1), libthai0 (= 0.1.28-4.1), libtiff5 (= 4.3.0-2), libtinfo6 (= 6.2+20210905-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtk8.6 (= 8.6.11.1-1), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-10ubuntu1), libubsan1 (= 11.2.0-10ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 248.3-1ubuntu8), libunistring2 (= 0.9.10-6), libuuid1 (= 2.36.1-8ubuntu2), libwebp6 (= 0.6.1-2.1build1), libwebpdemux2 (= 0.6.1-2.1build1), libwebpmux3 (= 0.6.1-2.1build1), libx11-6 (= 2:1.7.2-2), libx11-data (= 2:1.7.2-2), libxau6 (= 1:1.0.9-1build4), libxcb-render0 (= 1.14-3ubuntu2), libxcb-shm0 (= 1.14-3ubuntu2), libxcb1 (= 1.14-3ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu4), libxext6 (= 2:1.3.4-0ubuntu4), libxft2 (= 2.3.3-0ubuntu4), libxml2 (= 2.9.12+dfsg-5), libxrender1 (= 1:0.9.10-1build3), libxss1 (= 1:1.2.3-1build1), libxt6 (= 1:1.2.0-1build1), libyaml-0-2 (= 0.2.2-1build1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.13.0-19.19), login (= 1:4.8.1-1ubuntu9), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 16), m4 (= 1.4.18-5ubuntu1), mailcap (= 3.70ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), mime-support (= 3.66), ncurses-base (= 6.2+20210905-1), ncurses-bin (= 6.2+20210905-1), openssl (= 1.1.1l-1ubuntu1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), poppler-utils (= 21.06.1-1), procps (= 2:3.3.17-5ubuntu3), python-matplotlib-data (= 3.3.4-2), python3 (= 3.9.4-1ubuntu2), python3-all (= 3.9.4-1ubuntu2), python3-biopython (= 1.78+dfsg-5ubuntu1), python3-cycler (= 0.10.0-3), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-distutils (= 3.9.7-1), python3-future (= 0.18.2-5), python3-joblib (= 0.17.0-4), python3-kiwisolver (= 1.3.2-1), python3-lib2to3 (= 3.9.7-1), python3-matplotlib (= 3.3.4-2), python3-minimal (= 3.9.4-1ubuntu2), python3-networkx (= 2.4-4ubuntu1), python3-numpy (= 1:1.20.2-1ubuntu1), python3-pandas (= 1.1.5+dfsg-2), python3-pandas-lib (= 1.1.5+dfsg-2), python3-pil (= 8.3.2-1), python3-pkg-resources (= 58.2.0-1), python3-pomegranate (= 0.13.5-1), python3-pyfaidx (= 0.6.2-1), python3-pyparsing (= 2.4.7-1), python3-pysam (= 0.17.0+ds-2), python3-renderpm (= 3.6.1-1), python3-reportlab (= 3.6.1-1), python3-reportlab-accel (= 3.6.1-1), python3-scipy (= 1.6.0-2), python3-setuptools (= 58.2.0-1), python3-six (= 1.16.0-2), python3-tz (= 2021.3-1), python3-vcf (= 0.6.8+git20170215.476169c-8), python3-yaml (= 5.4.1-1), python3.10 (= 3.10.0-3), python3.10-minimal (= 3.10.0-3), python3.9 (= 3.9.7-4), python3.9-minimal (= 3.9.7-4), r-base-core (= 4.1.1-2), r-bioc-biocgenerics (= 0.38.0-1), r-bioc-dnacopy (= 1.66.0-1), readline-common (= 8.1-2build1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), ttf-bitstream-vera (= 1.10-8.1), tzdata (= 2021a-2ubuntu1), ucf (= 3.0043), unzip (= 6.0-26ubuntu2), util-linux (= 2.36.1-8ubuntu2), x11-common (= 1:7.7+23ubuntu1), xdg-utils (= 1.1.3-2ubuntu2), xz-utils (= 5.2.5-2build1), zip (= 3.0-12build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1634280066" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cnvkit_0.9.9-2_arm64.deb ------------------------ new Debian package, version 2.0. size 16135876 bytes: control archive=6017 bytes. 938 bytes, 15 lines control 16538 bytes, 189 lines md5sums 249 bytes, 12 lines * postinst #!/bin/sh 398 bytes, 12 lines * prerm #!/bin/sh Package: cnvkit Version: 0.9.9-2 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 69064 Depends: python3-biopython, python3-joblib, python3-matplotlib, python3-networkx, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Section: science Priority: optional Homepage: http://cnvkit.readthedocs.org Description: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 1479 Distribution: jammy-proposed Host Architecture: arm64 Install-Time: 186 Job: cnvkit_0.9.9-2.dsc Machine Architecture: arm64 Package: cnvkit Package-Time: 1671 Source-Version: 0.9.9-2 Space: n/a Status: successful Version: 0.9.9-2 -------------------------------------------------------------------------------- Finished at 2021-10-22T12:10:21Z Build needed 00:27:51, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292071 Scanning for processes to kill in build PACKAGEBUILD-22292071