https://launchpad.net/ubuntu/+source/cnvkit/0.9.6-3/+build/18529078 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-028 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 7 Jan 17:11:28 ntpdate[1901]: adjust time server 10.211.37.1 offset -0.000495 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18529078 --image-type chroot /home/buildd/filecache-default/e96c25c651525abc9f0cabeb95ea71010abf4ecb Creating target for build PACKAGEBUILD-18529078 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18529078 Starting target for build PACKAGEBUILD-18529078 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18529078 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18529078 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18529078 Updating target for build PACKAGEBUILD-18529078 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [107 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 Packages [967 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe amd64 Packages [8669 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 Packages [78.2 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [38.3 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 Packages [444 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [241 kB] Fetched 16.7 MB in 4s (4462 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 94 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After this operation, 51.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main amd64 libc6-dev amd64 2.30-0ubuntu3 [2549 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libc-dev-bin amd64 2.30-0ubuntu3 [71.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 linux-libc-dev amd64 5.4.0-9.12 [1082 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libisl22 amd64 0.22-2 [592 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libcc1-0 amd64 9.2.1-22ubuntu2 [48.8 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-x86-64-linux-gnu amd64 2.33.1-6ubuntu3 [1639 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libbinutils amd64 2.33.1-6ubuntu3 [474 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-common amd64 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 binutils amd64 2.33.1-6ubuntu3 [3400 B] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 gcc-9-base amd64 9.2.1-22ubuntu2 [19.0 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libgcc1 amd64 1:9.2.1-22ubuntu2 [40.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libgomp1 amd64 9.2.1-22ubuntu2 [89.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libitm1 amd64 9.2.1-22ubuntu2 [28.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libatomic1 amd64 9.2.1-22ubuntu2 [9232 B] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libasan5 amd64 9.2.1-22ubuntu2 [395 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 liblsan0 amd64 9.2.1-22ubuntu2 [139 kB] Get:17 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libtsan0 amd64 9.2.1-22ubuntu2 [301 kB] Get:18 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libubsan1 amd64 9.2.1-22ubuntu2 [130 kB] Get:19 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libquadmath0 amd64 9.2.1-22ubuntu2 [146 kB] Get:20 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 g++-9 amd64 9.2.1-22ubuntu2 [11.0 MB] Get:21 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libstdc++-9-dev amd64 9.2.1-22ubuntu2 [1709 kB] Get:22 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libgcc-9-dev amd64 9.2.1-22ubuntu2 [2360 kB] Get:23 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 gcc-9 amd64 9.2.1-22ubuntu2 [10.4 MB] Get:24 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 cpp-9 amd64 9.2.1-22ubuntu2 [9728 kB] Get:25 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libstdc++6 amd64 9.2.1-22ubuntu2 [511 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libc6 amd64 2.30-0ubuntu3 [2725 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 base-files amd64 11ubuntu2 [60.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 debianutils amd64 4.9.1 [85.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 bash amd64 5.0-5ubuntu1 [639 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 bsdutils amd64 1:2.34-0.1ubuntu4 [63.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 gzip amd64 1.10-0ubuntu4 [95.3 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 hostname amd64 3.23 [11.4 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-bin amd64 6.1+20191019-1ubuntu1 [172 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9 [3950 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 perl amd64 5.30.0-9 [224 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 perl-base amd64 5.30.0-9 [1511 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-1.0 amd64 1.0.8-2 [32.3 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid1 amd64 2.34-0.1ubuntu4 [137 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 libuuid1 amd64 2.34-0.1ubuntu4 [20.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libfdisk1 amd64 2.34-0.1ubuntu4 [175 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-8-0 amd64 10.34-7 [197 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libselinux1 amd64 3.0-1 [68.7 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libmount1 amd64 2.34-0.1ubuntu4 [149 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses6 amd64 6.1+20191019-1ubuntu1 [101 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libtinfo6 amd64 6.1+20191019-1ubuntu1 [85.9 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libncursesw6 amd64 6.1+20191019-1ubuntu1 [132 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libsmartcols1 amd64 2.34-0.1ubuntu4 [101 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 fdisk amd64 2.34-0.1ubuntu4 [120 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 util-linux amd64 2.34-0.1ubuntu4 [1022 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libdebconfclient0 amd64 0.250ubuntu2 [6336 B] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 base-passwd amd64 3.5.47 [47.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libc-bin amd64 2.30-0ubuntu3 [625 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 sysvinit-utils amd64 2.96-1ubuntu1 [20.8 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 liblz4-1 amd64 1.9.2-2 [55.9 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 systemd-sysv amd64 244-3ubuntu1 [9368 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libacl1 amd64 2.2.53-5ubuntu1 [18.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libapparmor1 amd64 2.13.3-7ubuntu1 [34.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libcap-ng0 amd64 0.7.9-2.1 [11.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit1 amd64 1:2.8.5-2ubuntu5 [39.1 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libcap2 amd64 1:2.27-1 [14.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libudev1 amd64 244-3ubuntu1 [76.3 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-2ubuntu7 [127 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 libjson-c4 amd64 0.13.1+dfsg-6 [29.2 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libcryptsetup12 amd64 2:2.2.2-1ubuntu1 [182 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libnettle7 amd64 3.5.1+really3.5.1-2 [114 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libhogweed5 amd64 3.5.1+really3.5.1-2 [138 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libp11-kit0 amd64 0.23.18.1-2 [189 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libtasn1-6 amd64 4.15.0-2 [37.7 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libgnutls30 amd64 3.6.11.1-2 [793 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libkmod2 amd64 26-3ubuntu1 [42.9 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libpam0g amd64 1.3.1-5ubuntu4 [55.4 kB] Get:77 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libseccomp2 amd64 2.4.2-2ubuntu2 [40.3 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 mount amd64 2.34-0.1ubuntu4 [115 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 systemd amd64 244-3ubuntu1 [3677 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libsystemd0 amd64 244-3ubuntu1 [260 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focal/main amd64 libsemanage-common all 3.0-1 [9880 B] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage1 amd64 3.0-1 [85.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libsqlite3-0 amd64 3.30.1-1ubuntu1 [540 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 gpg amd64 2.2.17-3ubuntu1 [479 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 gpgconf amd64 2.2.17-3ubuntu1 [124 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 gpg-agent amd64 2.2.17-3ubuntu1 [232 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile-bin amd64 1.16-1.1 [11.7 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile1 amd64 1.16-1.1 [6680 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.2 MB in 4s (18.8 MB/s) (Reading database ... 12741 files and directories currently 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Setting up libstdc++-9-dev:amd64 (9.2.1-22ubuntu2) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-22ubuntu2) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18529078 amd64 focal-proposed -c chroot:build-PACKAGEBUILD-18529078 --arch=amd64 --dist=focal-proposed --nolog -A cnvkit_0.9.6-3.dsc Initiating build PACKAGEBUILD-18529078 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-028.buildd +==============================================================================+ | cnvkit 0.9.6-3 (amd64) 07 Jan 2020 17:11 | +==============================================================================+ Package: cnvkit Version: 0.9.6-3 Source Version: 0.9.6-3 Distribution: focal-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/cnvkit-Ow55n2/cnvkit-0.9.6' with '<>' I: NOTICE: Log filtering will replace 'build/cnvkit-Ow55n2' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18529078/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cnvkit_0.9.6-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-CZJUEt/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-CZJUEt/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CZJUEt/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-CZJUEt/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CZJUEt/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-CZJUEt/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (0 B/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 packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-CZJUEt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14657 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), 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 (>= 0.9.0), r-bioc-dnacopy, poppler-utils Filtered Build-Depends: debhelper-compat (= 12), 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 (>= 0.9.0), r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'sbuild-build-depends-cnvkit-dummy' in '/<>/resolver-1gTeER/apt_archive/sbuild-build-depends-cnvkit-dummy.deb'. Ign:1 copy:/<>/resolver-1gTeER/apt_archive ./ InRelease Get:2 copy:/<>/resolver-1gTeER/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-1gTeER/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-1gTeER/apt_archive ./ Sources [320 B] Get:5 copy:/<>/resolver-1gTeER/apt_archive ./ Packages [647 B] Fetched 3086 B in 0s (0 B/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 packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libice6 libicu63 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler90 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal 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 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db 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-pyvcf python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-yaml python3.7 python3.7-minimal python3.8 python3.8-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 wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user 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-rdflib python3-renderpm python3-psycopg2 raxml samtools t-coffee wise w3-dtd-mathml python-cycler-doc python-future-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt4 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-networkx-doc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pandas-doc python3-statsmodels python-pil-doc python3-pil-dbg python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-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 krb5-locales poppler-data publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-tk python3-gdal python3-pydot python3-pygraphviz python3-numexpr python3-tables python3-xlrd python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-olefile python3-renderpm 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 bsdmainutils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-lyx gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libice6 libicu63 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpoppler90 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal 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 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db 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-pyvcf python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-tz python3-yaml python3.7 python3.7-minimal python3.8 python3.8-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, 171 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 480 MB of additional disk space will be used. Get:1 copy:/<>/resolver-1gTeER/apt_archive ./ sbuild-build-depends-cnvkit-dummy 0.invalid.0 [976 B] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.7-minimal amd64 3.7.6-1 [546 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libexpat1 amd64 2.2.9-1 [73.3 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.7-minimal amd64 3.7.6-1 [1766 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 python3-minimal amd64 3.7.5-1ubuntu1 [23.3 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.7-stdlib amd64 3.7.6-1 [1735 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.7 amd64 3.7.6-1 [304 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3-stdlib amd64 3.7.5-1ubuntu1 [6844 B] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 python3 amd64 3.7.5-1ubuntu1 [47.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 groff-base amd64 1.22.4-4 [865 kB] Get:17 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpipeline1 amd64 1.5.2-1 [27.7 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 man-db amd64 2.9.0-2 [1114 kB] Get:19 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.8-minimal amd64 3.8.1-2 [704 kB] Get:20 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.8-minimal amd64 3.8.1-2 [1890 kB] Get:21 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amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:43 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libxcb1 amd64 1.13.1-3 [45.3 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-data all 2:1.6.8-1 [113 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-6 amd64 2:1.6.8-1 [573 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 autoconf all 2.69-11ubuntu1 [321 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:51 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 automake all 1:1.16.1-4ubuntu4 [522 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 autopoint all 0.19.8.1-10 [412 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 libtool all 2.4.6-11 [194 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 dh-autoreconf all 19 [16.1 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 libfile-stripnondeterminism-perl all 1.6.3-1 [16.0 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 dh-strip-nondeterminism all 1.6.3-1 [5224 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 dwz amd64 0.13-5 [151 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 gettext amd64 0.19.8.1-10 [897 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 po-debconf all 1.0.21 [233 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 debhelper all 12.7.1ubuntu1 [875 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 python3-lib2to3 all 3.8.0-1 [75.6 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 python3-distutils all 3.8.0-1 [142 kB] Get:68 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 dh-python all 4.20191017ubuntu2 [88.4 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libfreetype6 amd64 2.10.1-2 [341 kB] Get:70 http://ftpmaster.internal/ubuntu focal/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu2 [114 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig amd64 2.13.1-2ubuntu2 [171 kB] Get:74 http://ftpmaster.internal/ubuntu focal/universe amd64 fonts-lyx all 2.3.3-2 [154 kB] Get:75 http://ftpmaster.internal/ubuntu focal/universe amd64 help2man amd64 1.47.12 [172 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-1 [41.9 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-1 [181 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 libblas3 amd64 3.9.0-1 [142 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 libbrotli1 amd64 1.0.7-6 [267 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libpixman-1-0 amd64 0.38.4-0ubuntu1 [227 kB] Get:81 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libxcb-render0 amd64 1.13.1-3 [14.8 kB] Get:82 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libxcb-shm0 amd64 1.13.1-3 [5576 B] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo2 amd64 1.16.0-4ubuntu1 [583 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-1 [29.7 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-1 [87.8 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-1 [47.9 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-1 [107 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-1 [207 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-1 [15.1 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-1 [96.6 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:94 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libldap-common all 2.4.48+dfsg-1ubuntu4 [16.9 kB] Get:95 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libldap-2.4-2 amd64 2.4.48+dfsg-1ubuntu4 [155 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 libnghttp2-14 amd64 1.40.0-1 [78.1 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 libssh-4 amd64 0.9.0-1ubuntu5 [196 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl3-gnutls amd64 7.66.0-1ubuntu1 [231 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4 amd64 7.66.0-1ubuntu1 [232 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main amd64 libdatrie1 amd64 0.2.12-3 [18.7 kB] Get:102 http://ftpmaster.internal/ubuntu focal/universe amd64 libdeflate0 amd64 1.5-1 [87.2 kB] Get:103 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libgfortran5 amd64 9.2.1-22ubuntu2 [642 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main amd64 libgraphite2-3 amd64 1.3.13-11 [73.7 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main amd64 libharfbuzz0b amd64 2.6.4-1ubuntu1 [391 kB] Get:106 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 libhts3 amd64 1.10.2-2 [358 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main amd64 x11-common all 1:7.7+19ubuntu12 [22.4 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main amd64 libice6 amd64 2:1.0.10-0ubuntu1 [41.0 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main amd64 libimagequant0 amd64 2.12.2-1.1 [31.4 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu1 [118 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:112 http://ftpmaster.internal/ubuntu focal/main amd64 libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:113 http://ftpmaster.internal/ubuntu focal/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main amd64 liblapack3 amd64 3.9.0-1 [2155 kB] Get:115 http://ftpmaster.internal/ubuntu focal/universe amd64 liblbfgsb0 amd64 3.0+dfsg.3-7 [29.4 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main amd64 liblcms2-2 amd64 2.9-4 [140 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main amd64 libnspr4 amd64 2:4.24-1 [107 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main amd64 libnss3 amd64 2:3.47-1ubuntu2 [1167 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main amd64 libthai-data all 0.1.28-3 [134 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main amd64 libthai0 amd64 0.1.28-3 [18.1 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main amd64 libpango-1.0-0 amd64 1.44.7-1 [161 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main amd64 libpangoft2-1.0-0 amd64 1.44.7-1 [34.7 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main amd64 libpangocairo-1.0-0 amd64 1.44.7-1 [24.8 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper1 amd64 1.1.28 [13.0 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper-utils amd64 1.1.28 [8400 B] Get:126 http://ftpmaster.internal/ubuntu focal/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main amd64 libtiff5 amd64 4.1.0+git191117-1 [162 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main amd64 libpoppler90 amd64 0.80.0-0ubuntu4 [914 kB] Get:130 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 libpython3.8-stdlib amd64 3.8.1-2 [1666 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main amd64 libsm6 amd64 2:1.2.3-1 [16.1 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [902 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main amd64 libxft2 amd64 2.3.3-0ubuntu1 [39.2 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main amd64 libxss1 amd64 1:1.2.3-1 [8140 B] Get:135 http://ftpmaster.internal/ubuntu focal/main amd64 libtk8.6 amd64 8.6.10-1 [714 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main amd64 libwebpdemux2 amd64 0.6.1-2 [9472 B] Get:137 http://ftpmaster.internal/ubuntu focal/main amd64 libwebpmux3 amd64 0.6.1-2 [19.6 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main amd64 poppler-utils amd64 0.80.0-0ubuntu4 [172 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe amd64 python-matplotlib-data all 3.0.2-2ubuntu1 [3775 kB] Get:141 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3.8 amd64 3.8.1-2 [360 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main amd64 python3-all amd64 3.7.5-1ubuntu1 [1120 B] Get:143 http://ftpmaster.internal/ubuntu focal/main amd64 python3-numpy amd64 1:1.17.4-3ubuntu2 [6135 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main amd64 python3-reportlab-accel amd64 3.5.31-1 [23.9 kB] Get:145 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3-pil amd64 7.0.0-2 [375 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main amd64 python3-reportlab all 3.5.31-1 [531 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-biopython amd64 1.76+dfsg-1 [1416 kB] Get:148 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-cycler all 0.10.0-2 [8024 B] Get:149 http://ftpmaster.internal/ubuntu focal/main amd64 python3-dateutil all 2.7.3-3ubuntu1 [63.3 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main amd64 python3-decorator all 4.3.0-1.1build1 [9652 B] Get:151 http://ftpmaster.internal/ubuntu focal/main amd64 python3-future all 0.16.0-1 [334 kB] Get:152 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-joblib all 0.14.0-2 [189 kB] Get:153 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-kiwisolver amd64 1.0.1-2build3 [86.7 kB] Get:154 http://ftpmaster.internal/ubuntu focal/main amd64 python3-pyparsing all 2.4.2-1 [58.8 kB] Get:155 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-matplotlib amd64 3.0.2-2ubuntu1 [4601 kB] Get:156 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3-networkx all 2.4-3 [856 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main amd64 python3-tz all 2019.3-1 [24.4 kB] Get:158 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-pandas-lib amd64 0.25.3+dfsg-4 [8384 kB] Get:159 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-pandas all 0.25.3+dfsg-4 [1967 kB] Get:160 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 python3-scipy amd64 1.3.3-3 [13.6 MB] Get:161 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-pomegranate amd64 0.12.0+dfsg-2 [3872 kB] Get:162 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-pyfaidx all 0.5.5.2-2 [25.6 kB] Get:163 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 python3-pysam amd64 0.15.3+ds-5 [2776 kB] Get:164 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-pyvcf amd64 0.6.8+git20170215.476169c-2 [57.2 kB] Get:165 http://ftpmaster.internal/ubuntu focal-proposed/main amd64 python3-setuptools all 44.0.0-1 [257 kB] Get:166 http://ftpmaster.internal/ubuntu focal/main amd64 zip amd64 3.0-11build1 [167 kB] Get:167 http://ftpmaster.internal/ubuntu focal/main amd64 unzip amd64 6.0-25ubuntu1 [169 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main amd64 xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:169 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 r-base-core amd64 3.6.2-2 [24.6 MB] Get:170 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 r-bioc-biocgenerics all 0.32.0-1 [639 kB] Get:171 http://ftpmaster.internal/ubuntu focal-proposed/universe amd64 r-bioc-dnacopy amd64 1.60.0-1 [420 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 118 MB in 4s (30.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14657 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.6-1_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.6-1_amd64.deb ... Unpacking python3.7-minimal (3.7.6-1) ... Setting up libpython3.7-minimal:amd64 (3.7.6-1) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.7-minimal (3.7.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 14920 files and directories currently installed.) 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Setting up x11-common (1:7.7+19ubuntu12) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up libmagic1:amd64 (1:5.37-6ubuntu1) ... Setting up libdeflate0 (1.5-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.37-6ubuntu1) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu4) ... Setting up libjbig0:amd64 (2.1-3.1build1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libfreetype6:amd64 (2.10.1-2) ... Setting up libx11-data (2:1.6.8-1) ... Setting up libnspr4:amd64 (2:4.24-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libfribidi0:amd64 (1.0.8-2) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libtcl8.6:amd64 (8.6.10+dfsg-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up libjpeg-turbo8:amd64 (2.0.3-0ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up libgfortran5:amd64 (9.2.1-22ubuntu2) ... Setting up libroken18-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up python3.8-minimal (3.8.1-2) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:amd64 (2.6.4-1ubuntu1) ... Setting up libthai-data (0.1.28-3) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libpython3.8-stdlib:amd64 (3.8.1-2) ... Setting up python3.8 (3.8.1-2) ... Setting up python-matplotlib-data (3.0.2-2ubuntu1) ... Setting up libwebpmux3:amd64 (0.6.1-2) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1build1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8ubuntu1) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libheimbase1-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:amd64 (2:1.0.10-0ubuntu1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... Setting up libpython3.7-stdlib:amd64 (3.7.6-1) ... Setting up liblapack3:amd64 (3.9.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.13.1-3) ... Setting up libtool (2.4.6-11) ... Setting up libxcb-render0:amd64 (1.13.1-3) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libwebpdemux2:amd64 (0.6.1-2) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libnss3:amd64 (2:3.47-1ubuntu2) ... Setting up libxcb-shm0:amd64 (1.13.1-3) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up help2man (1.47.12) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libssh-4:amd64 (0.9.0-1ubuntu5) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libx11-6:amd64 (2:1.6.8-1) ... Setting up libtiff5:amd64 (4.1.0+git191117-1) ... Setting up libfontconfig1:amd64 (2.13.1-2ubuntu2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3-stdlib:amd64 (3.7.5-1ubuntu1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-7) ... Setting up automake (1:1.16.1-4ubuntu4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.6-1) ... Setting up fontconfig (2.13.1-2ubuntu2) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libpango-1.0-0:amd64 (1.44.7-1) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up man-db (2.9.0-2) ... 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:amd64 (1.16.0-4ubuntu1) ... Setting up python3-tz (2019.3-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.13.0-1build1) ... Setting up python3-pil:amd64 (7.0.0-2) ... Setting up python3-decorator (4.3.0-1.1build1) ... Setting up python3-pyparsing (2.4.2-1) ... Setting up python3-cycler (0.10.0-2) ... Setting up python3-reportlab-accel:amd64 (3.5.31-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up python3-reportlab (3.5.31-1) ... Setting up libpoppler90:amd64 (0.80.0-0ubuntu4) ... Setting up python3-dateutil (2.7.3-3ubuntu1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up poppler-utils (0.80.0-0ubuntu4) ... Setting up libpangoft2-1.0-0:amd64 (1.44.7-1) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.44.7-1) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up python3-pkg-resources (44.0.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu2) ... Setting up python3-pyfaidx (0.5.5.2-2) ... Setting up libxft2:amd64 (2.3.3-0ubuntu1) ... Setting up python3-setuptools (44.0.0-1) ... Setting up python3-joblib (0.14.0-2) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.10-1) ... Setting up python3-all (3.7.5-1ubuntu1) ... Setting up python3-yaml (5.2-1) ... Setting up python3-networkx (2.4-3) ... /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 libheimntlm0-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up python3-pyvcf (0.6.8+git20170215.476169c-2) ... Setting up python3-kiwisolver (1.0.1-2build3) ... Setting up python3-numpy (1:1.17.4-3ubuntu2) ... Setting up python3-future (0.16.0-1) ... 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 (1.76+dfsg-1) ... Setting up python3-matplotlib (3.0.2-2ubuntu1) ... /usr/lib/python3/dist-packages/matplotlib/backends/qt_editor/figureoptions.py:220: SyntaxWarning: "is not" with a literal. Did you mean "!="? if marker is not 'none': /usr/lib/python3/dist-packages/matplotlib/pyplot.py:2201: SyntaxWarning: "is" with a literal. Did you mean "=="? if fignum is False or fignum is 0: Setting up python3-scipy (1.3.3-3) ... Setting up python3-pomegranate (0.12.0+dfsg-2) ... Setting up python3-pandas-lib (0.25.3+dfsg-4) ... Setting up libldap-2.4-2:amd64 (2.4.48+dfsg-1ubuntu4) ... Setting up libcurl3-gnutls:amd64 (7.66.0-1ubuntu1) ... Setting up python3-pandas (0.25.3+dfsg-4) ... /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 /usr/lib/python3/dist-packages/pandas/tests/frame/test_alter_axes.py:241: SyntaxWarning: "is" with a literal. Did you mean "=="? False if (keys[0] is "A" and keys[1] is "A") else drop # noqa: F632 Setting up libcurl4:amd64 (7.66.0-1ubuntu1) ... Setting up libhts3:amd64 (1.10.2-2) ... Setting up python3-pysam (0.15.3+ds-5) ... Setting up r-base-core (3.6.2-2) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-biocgenerics (0.32.0-1) ... Setting up r-bioc-dnacopy (1.60.0-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up sbuild-build-depends-cnvkit-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... Processing triggers for systemd (244-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic amd64 (x86_64) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-22ubuntu2 gcc-9_9.2.1-22ubuntu2 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-22ubuntu2 libstdc++6_9.2.1-22ubuntu2 linux-libc-dev_5.4.0-9.12 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-x86-64-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-22ubuntu2 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu2 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu4 file_1:5.37-6ubuntu1 findutils_4.6.0+git+20190209-2ubuntu1 fontconfig_2.13.1-2ubuntu2 fontconfig-config_2.13.1-2ubuntu2 fonts-lyx_2.3.3-2 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-22ubuntu2 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-22ubuntu2 gcc-9-base_9.2.1-22ubuntu2 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 help2man_1.47.12 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.5 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-22ubuntu2 libasn1-8-heimdal_7.7.0+dfsg-1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-22ubuntu2 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.1-6ubuntu3 libblas3_3.9.0-1 libblkid1_2.34-0.1ubuntu4 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcairo2_1.16.0-4ubuntu1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcc1-0_9.2.1-22ubuntu2 libcom-err2_1.45.3-4ubuntu2 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libcurl3-gnutls_7.66.0-1ubuntu1 libcurl4_7.66.0-1ubuntu1 libdatrie1_0.2.12-3 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.1ubuntu1 libdeflate0_1.5-1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1build1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfontconfig1_2.13.1-2ubuntu2 libfreetype6_2.10.1-2 libfribidi0_1.0.8-2 libgcc-9-dev_9.2.1-22ubuntu2 libgcc1_1:9.2.1-22ubuntu2 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-22ubuntu2 libglib2.0-0_2.63.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22ubuntu2 libgpg-error0_1.36-7 libgraphite2-3_1.3.13-11 libgssapi-krb5-2_1.17-6 libgssapi3-heimdal_7.7.0+dfsg-1 libharfbuzz0b_2.6.4-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-2 libhx509-5-heimdal_7.7.0+dfsg-1 libice6_2:1.0.10-0ubuntu1 libicu63_63.2-2 libidn2-0_2.2.0-2 libimagequant0_2.12.2-1.1 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_9.2.1-22ubuntu2 libjbig0_2.1-3.1build1 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libjs-jquery_3.3.1~dfsg-3 libjs-jquery-ui_1.12.1+dfsg-5 libjson-c4_0.13.1+dfsg-6 libk5crypto3_1.17-6 libkeyutils1_1.6-6ubuntu1 libkmod2_26-3ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 liblapack3_3.9.0-1 liblbfgsb0_3.0+dfsg.3-7 liblcms2-2_2.9-4 libldap-2.4-2_2.4.48+dfsg-1ubuntu4 libldap-common_2.4.48+dfsg-1ubuntu4 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_9.2.1-22ubuntu2 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6ubuntu1 libmagic1_1:5.37-6ubuntu1 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libnspr4_2:4.24-1 libnss3_2:3.47-1ubuntu2 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpango-1.0-0_1.44.7-1 libpangocairo-1.0-0_1.44.7-1 libpangoft2-1.0-0_1.44.7-1 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpixman-1-0_0.38.4-0ubuntu1 libpng16-16_1.6.37-1 libpoppler90_0.80.0-0ubuntu4 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libpython3.8-minimal_3.8.1-2 libpython3.8-stdlib_3.8.1-2 libquadmath0_9.2.1-22ubuntu2 libreadline8_8.0-3 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.34-0.1ubuntu4 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssh-4_0.9.0-1ubuntu5 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-22ubuntu2 libstdc++6_9.2.1-22ubuntu2 libsub-override-perl_0.09-2 libsystemd0_244-3ubuntu1 libtasn1-6_4.15.0-2 libtcl8.6_8.6.10+dfsg-1 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-1 libtinfo6_6.1+20191019-1ubuntu1 libtk8.6_8.6.10-1 libtool_2.4.6-11 libtsan0_9.2.1-22ubuntu2 libubsan1_9.2.1-22ubuntu2 libuchardet0_0.0.6-3 libudev1_244-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.9-0ubuntu1 libxcb-render0_1.13.1-3 libxcb-shm0_1.13.1-3 libxcb1_1.13.1-3 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxft2_2.3.3-0ubuntu1 libxml2_2.9.4+dfsg1-8ubuntu1 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.4.0-9.12 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 poppler-utils_0.80.0-0ubuntu4 procps_2:3.3.15-2ubuntu3 python-matplotlib-data_3.0.2-2ubuntu1 python3_3.7.5-1ubuntu1 python3-all_3.7.5-1ubuntu1 python3-biopython_1.76+dfsg-1 python3-cycler_0.10.0-2 python3-dateutil_2.7.3-3ubuntu1 python3-decorator_4.3.0-1.1build1 python3-distutils_3.8.0-1 python3-future_0.16.0-1 python3-joblib_0.14.0-2 python3-kiwisolver_1.0.1-2build3 python3-lib2to3_3.8.0-1 python3-matplotlib_3.0.2-2ubuntu1 python3-minimal_3.7.5-1ubuntu1 python3-networkx_2.4-3 python3-numpy_1:1.17.4-3ubuntu2 python3-pandas_0.25.3+dfsg-4 python3-pandas-lib_0.25.3+dfsg-4 python3-pil_7.0.0-2 python3-pkg-resources_44.0.0-1 python3-pomegranate_0.12.0+dfsg-2 python3-pyfaidx_0.5.5.2-2 python3-pyparsing_2.4.2-1 python3-pysam_0.15.3+ds-5 python3-pyvcf_0.6.8+git20170215.476169c-2 python3-reportlab_3.5.31-1 python3-reportlab-accel_3.5.31-1 python3-scipy_1.3.3-3 python3-setuptools_44.0.0-1 python3-six_1.13.0-1build1 python3-tz_2019.3-1 python3-yaml_5.2-1 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 python3.8_3.8.1-2 python3.8-minimal_3.8.1-2 r-base-core_3.6.2-2 r-bioc-biocgenerics_0.32.0-1 r-bioc-dnacopy_1.60.0-1 readline-common_8.0-3 sbuild-build-depends-cnvkit-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 ttf-bitstream-vera_1.10-8 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 unzip_6.0-25ubuntu1 util-linux_2.34-0.1ubuntu4 x11-common_1:7.7+19ubuntu12 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Jan 7 10:49:59 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cnvkit_0.9.6-3.dsc dpkg-source: info: extracting cnvkit in cnvkit-0.9.6 dpkg-source: info: unpacking cnvkit_0.9.6.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.6-3.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 disc 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-18529078 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18529078 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18529078 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 0.9.6-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot 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:217: python3.8 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.8_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.7_cnvkit/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.7' 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 build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config I: pybuild base:217: python3.7 setup.py config 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:217: /usr/bin/python3.8 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/_version.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/batch.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/params.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/reference.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/importers.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/core.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/access.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/call.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/export.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/rna.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/vary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/plots.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/ztest.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/fix.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/reports.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/commands.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/target.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib creating /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm_learn.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation creating /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/intersect.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/chromsort.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/subdivide.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/subtract.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/gary.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/combiners.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome copying skgenome/merge.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome creating /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio running build_scripts creating build creating build/scripts-3.8 copying and adjusting ./cnvkit -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_ztest -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-reference2targets -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-guess_baits -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-cnv_updater -> build/scripts-3.8 copying ./scripts/snpfilter.sh -> build/scripts-3.8 copying and adjusting ./scripts/cnvkit-skg_convert -> build/scripts-3.8 changing mode of build/scripts-3.8/cnvkit from 664 to 775 changing mode of build/scripts-3.8/cnvkit-cnv_expression_correlate from 664 to 775 changing mode of build/scripts-3.8/cnvkit-cnv_ztest from 664 to 775 changing mode of build/scripts-3.8/cnvkit-cnv_annotate from 664 to 775 changing mode of build/scripts-3.8/cnvkit-reference2targets from 664 to 775 changing mode of build/scripts-3.8/cnvkit-guess_baits from 664 to 775 changing mode of build/scripts-3.8/cnvkit-cnv_updater from 664 to 775 changing mode of build/scripts-3.8/cnvkit-skg_convert from 664 to 775 I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/metrics.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/import_rna.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/scatter.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/_version.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segmetrics.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/batch.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/params.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cnary.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reference.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/samutil.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/descriptives.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/importers.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/core.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/access.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/call.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/export.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/antitarget.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/rna.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/__init__.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/parallel.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/autobin.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/vary.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/diagram.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/plots.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/smoothing.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/ztest.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/fix.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/reports.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/segfilters.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/commands.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/cmdutil.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/target.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/heatmap.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib copying cnvlib/coverage.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib creating /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm_learn.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/none.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation creating /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/intersect.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/rangelabel.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/chromsort.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subdivide.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/subtract.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/__init__.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/gary.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/combiners.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome copying skgenome/merge.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome creating /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/textcoord.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/gff.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seg.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/__init__.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/genepred.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfio.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/picard.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/tab.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/util.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/bedio.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio copying skgenome/tabio/seqdict.py -> /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio running build_scripts creating build/scripts-3.7 copying and adjusting ./cnvkit -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_expression_correlate -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_ztest -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_annotate -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-reference2targets -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-guess_baits -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-cnv_updater -> build/scripts-3.7 copying ./scripts/snpfilter.sh -> build/scripts-3.7 copying and adjusting ./scripts/cnvkit-skg_convert -> build/scripts-3.7 changing mode of build/scripts-3.7/cnvkit from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_expression_correlate from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_ztest from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_annotate from 664 to 775 changing mode of build/scripts-3.7/cnvkit-reference2targets from 664 to 775 changing mode of build/scripts-3.7/cnvkit-guess_baits from 664 to 775 changing mode of build/scripts-3.7/cnvkit-cnv_updater from 664 to 775 changing mode of build/scripts-3.7/cnvkit-skg_convert from 664 to 775 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 -j4 make[2]: Entering directory '/<>/test' python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-20_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-5_5.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Created directory build/ Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_2.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/p2-9_5.targetcoverage.cnn with 6646 regions python3 ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ Wrote build/p2-9_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/p2-20_5.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 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=67.2 x 0.532 = 35.7) --> assuming male Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=38.7 x 0.532 = 20.6) --> assuming male Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=94.8 x 0.532 = 50.4) --> assuming male Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=6.53 x 0.809 = 5.28) --> assuming male Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=9.76 x 0.895 = 8.74) --> assuming male Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=18.1 x 0.895 = 16.2) --> assuming male Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Calculating average bin coverages WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' python3 ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions python3 ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ python3 ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions Calculating bin spreads Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 89 (1.3392%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) NOTCH2 chr1:120572470-120572622 log2=-2.599 spread=1.522 GAK chr4:896278-896357 log2=-1.523 spread=1.267 MAP3K1 chr5:56111354-56111894 log2=-1.492 spread=1.060 FLT4 chr5:180076418-180076603 log2=-2.232 spread=1.421 DOM3Z chr6:31938905-31939081 log2=-20.033 spread=0.045 " chr6:31939599-31940313 log2=-19.608 spread=0.181 STK19 chr6:31940351-31940562 log2=-19.003 spread=0.189 " chr6:31946632-31946824 log2=-20.060 spread=0.088 " chr6:31947142-31947366 log2=-20.128 spread=0.065 " chr6:31948176-31948360 log2=-19.992 spread=0.148 " chr6:31948382-31948612 log2=-19.780 spread=0.162 " chr6:31948730-31949253 log2=-20.063 spread=0.020 NOTCH4 chr6:32163159-32163956 log2=-19.331 spread=0.202 " chr6:32164046-32164227 log2=-19.777 spread=0.180 " chr6:32164652-32164888 log2=-19.995 spread=0.151 " chr6:32165021-32165403 log2=-19.643 spread=0.195 " chr6:32166163-32166545 log2=-20.057 spread=0.076 " chr6:32166648-32166962 log2=-3.526 spread=5.774 " chr6:32168554-32168821 log2=-19.621 spread=0.193 " chr6:32168844-32169306 log2=-19.700 spread=0.164 " chr6:32169801-32170391 log2=-19.433 spread=0.206 " chr6:32171492-32171691 log2=-20.108 spread=0.103 " chr6:32171861-32172198 log2=-3.146 spread=7.284 " chr6:32178478-32178749 log2=-19.934 spread=0.167 " chr6:32180197-32180441 log2=-10.912 spread=9.531 " chr6:32180544-32180722 log2=-19.700 spread=0.182 " chr6:32180857-32181062 log2=-19.591 spread=0.214 " chr6:32181411-32181646 log2=-19.979 spread=0.168 " chr6:32181832-32182066 log2=-19.971 spread=0.174 " chr6:32182948-32183194 log2=-19.947 spread=0.171 " chr6:32184667-32185079 log2=-19.931 spread=0.162 " chr6:32185720-32185919 log2=-19.724 spread=0.192 " chr6:32187317-32187601 log2=-19.783 spread=0.171 " chr6:32187871-32188094 log2=-19.686 spread=0.190 " chr6:32188127-32188451 log2=-19.636 spread=0.165 " chr6:32188481-32188693 log2=-19.906 spread=0.130 " chr6:32188704-32189133 log2=-19.522 spread=0.199 " chr6:32190258-32190616 log2=-19.586 spread=0.207 " chr6:32190724-32190908 log2=-19.562 spread=0.218 " chr6:32191570-32191668 log2=-19.792 spread=0.174 " chr6:32191676-32191753 log2=-19.393 spread=0.201 CGH chr7:52520101-52520286 log2=-1.534 spread=1.178 SMO chr7:128828938-128829041 log2=-2.070 spread=1.324 GPR124 chr8:37654740-37655077 log2=-1.623 spread=1.026 GPSM1 chr9:139222089-139222248 log2=-4.896 spread=2.116 MRC1 chr10:18136438-18136613 log2=-1.967 spread=3.254 RET chr10:43572644-43572830 log2=-1.394 spread=1.097 FLT3 chr13:28674525-28674708 log2=-2.268 spread=1.749 IRS2 chr13:110438332-110438432 log2=-3.655 spread=2.330 CGH chr14:19220933-19221047 log2=-1.234 spread=1.211 MAP3K9 chr14:71275790-71275923 log2=-2.828 spread=1.943 LTK chr15:41803310-41803809 log2=-1.970 spread=1.452 PDPK1 chr16:2588022-2588201 log2=-1.783 spread=1.088 " chr16:2611404-2611585 log2=-5.189 spread=1.939 " chr16:2611721-2611943 log2=-11.822 spread=9.176 " chr16:2615504-2615725 log2=-20.129 spread=0.003 " chr16:2616307-2616486 log2=-20.077 spread=0.072 " chr16:2631267-2631414 log2=-20.027 spread=0.061 " chr16:2631583-2631734 log2=-20.122 spread=0.087 " chr16:2633363-2633616 log2=-20.108 spread=0.092 BOLA2B chr16:29466011-29466278 log2=-19.007 spread=0.177 MAP2K4 chr17:11924151-11924355 log2=-2.111 spread=1.902 GIPC3 chr19:3585549-3585853 log2=-1.530 spread=1.093 INSR chr19:7293751-7294042 log2=-2.032 spread=1.542 NOTCH3 chr19:15311544-15311749 log2=-1.901 spread=1.207 CD79A chr19:42384673-42384848 log2=-1.888 spread=1.229 CRLF2 chrX:1314835-1315039 log2=-20.125 spread=0.029 " chrX:1317372-1317594 log2=-20.136 spread=0.045 " chrX:1321225-1321435 log2=-19.869 spread=0.196 " chrX:1325274-1325530 log2=-20.131 spread=0.012 " chrX:1327651-1327830 log2=-20.012 spread=0.030 " chrX:1331391-1331576 log2=-20.024 spread=0.051 CGH chrY:2654543-2654722 log2=-4.357 spread=4.442 " chrY:3023482-3023672 log2=-4.960 spread=6.784 " chrY:4564417-4564597 log2=-11.686 spread=9.039 " chrY:7540620-7540741 log2=-5.016 spread=6.755 " chrY:9008607-9008759 log2=-12.124 spread=8.796 " chrY:13131970-13132039 log2=-20.071 spread=0.102 " chrY:13199435-13199623 log2=-4.281 spread=6.165 " chrY:15007107-15007258 log2=-6.946 spread=7.403 " chrY:16504318-16504496 log2=-5.090 spread=6.641 " chrY:18022729-18022918 log2=-5.529 spread=6.991 " chrY:19506485-19506650 log2=-11.896 spread=8.895 " chrY:21033918-21034071 log2=-20.101 spread=0.087 " chrY:22554204-22554385 log2=-6.070 spread=7.225 " chrY:24000593-24000773 log2=-4.446 spread=4.603 " chrY:28462977-28463157 log2=-5.435 spread=7.074 " chrY:28463435-28463622 log2=-11.305 spread=9.238 " chrY:28514033-28514208 log2=-12.104 spread=8.739 Antitargets: 111 (0.8835%) 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 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 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 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 Processing target: p2-20_2 Processing target: p2-5_5 Keeping 6557 of 6646 bins Processing target: p2-9_2 Correcting for GC bias... Processing target: p2-20_1 Correcting for density bias... Keeping 6557 of 6646 bins Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for GC bias... Correcting for density bias... Correcting for density bias... Keeping 6557 of 6646 bins Correcting for GC bias... Processing antitarget: p2-20_2 Correcting for density bias... Processing antitarget: p2-5_5 Processing antitarget: p2-9_2 Keeping 12452 of 12563 bins Correcting for GC bias... Keeping 12452 of 12563 bins WARNING: Skipping correction for RepeatMasker bias Keeping 12452 of 12563 bins Processing antitarget: p2-20_1 Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Targets are 1.04 x more variable than antitargets Keeping 12452 of 12563 bins Correcting for GC bias... Targets are 1.09 x more variable than antitargets Targets are 1.34 x more variable than antitargets WARNING: Skipping correction for RepeatMasker bias Wrote build/p2-20_2.cnr with 19009 regions Targets are 1.08 x more variable than antitargets Wrote build/p2-5_5.cnr with 19009 regions Wrote build/p2-9_2.cnr with 19009 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 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 Wrote build/p2-20_1.cnr with 19009 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 python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns Processing target: p2-20_3 Processing target: p2-20_4 Keeping 6557 of 6646 bins Processing target: p2-20_5 Correcting for GC bias... Keeping 6557 of 6646 bins Correcting for density bias... Correcting for GC bias... Keeping 6557 of 6646 bins Correcting for density bias... Correcting for GC bias... Correcting for density bias... Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Processing antitarget: p2-20_3 Processing antitarget: p2-20_4 Processing antitarget: p2-20_5 Keeping 12452 of 12563 bins Correcting for GC bias... Keeping 12452 of 12563 bins Keeping 12452 of 12563 bins WARNING: Skipping correction for RepeatMasker bias Correcting for GC bias... Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias WARNING: Skipping correction for RepeatMasker bias Antitargets are 1.01 x more variable than targets Targets are 1.60 x more variable than antitargets Targets are 1.18 x more variable than antitargets Wrote build/p2-20_3.cnr with 19009 regions Wrote build/p2-20_5.cnr with 19009 regions Wrote build/p2-20_4.cnr with 19009 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Dropped 1 / 966 bins on chromosome chr6 Wrote build/p2-5_5.cns with 49 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns Dropped 1 / 5 bins on chromosome chrY Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Wrote build/p2-9_2.cns with 57 regions Wrote build/p2-20_1.cns with 78 regions python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns python3 ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Wrote build/p2-20_2.cns with 77 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 Segmenting with method 'cbs', significance threshold 0.01, in 2 processes Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 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 Wrote build/p2-20_3.cns with 48 regions 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 Wrote build/p2-20_5.cns with 64 regions 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 Wrote build/p2-20_4.cns with 65 regions Showing 1498 probes and 0 selected genes in region chr1 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 Wrote p2-9_2-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 Wrote p2-9_2-chr1-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 Showing 203 probes and 0 selected genes in region chr21 Wrote p2-9_2-chr21-scatter.pdf python3 ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Showing 341 probes and 25 selected genes in region chr9:149999-45000000 Showing 186 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-chr9p-scatter.pdf Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf python3 ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf Detected file format: bed Showing 43 probes and 3 selected genes in region chr9:2000000-4000000 python3 ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf Showing 54 probes and 5 selected genes in region chr9:8000000-12000000 python3 ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_2 as male Wrote p2-5_5-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf Wrote p2-20_1-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Wrote p2-9_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Treating sample p2-5_5 as male Wrote p2-5_5-cbs-diagram.pdf Wrote p2-20_2-diagram.pdf python3 ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o 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 Treating sample p2-9_2 as male Wrote p2-9_2-cbs-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 Treating sample p2-20_1 as male Wrote p2-20_1-cbs-diagram.pdf Treating sample p2-20_2 as male 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 Wrote p2-20_2-cbs-diagram.pdf Treating sample p2-5_5 as male 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 Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_2 as male Wrote p2-5_5-both-diagram.pdf 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 Wrote p2-9_2-both-diagram.pdf python3 ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_2 as male Treating sample p2-20_3 as male Treating sample p2-20_4 as male Treating sample p2-20_5 as male Wrote p2-20_2-both-diagram.pdf Wrote p2-20_1-both-diagram.pdf python3 ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o 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 Found 1 gene breakpoints Wrote p2-9_2-breaks.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 Wrote heatmap-picard.pdf Treating sample p2-9_2 as male 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 Wrote gender-picard.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 Found 322 gene-level gains and losses Wrote p2-9_2-genemetrics.txt Wrote p2-all.seg python3 ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o 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 Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Wrote p2-9_2.nexus python3 ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Treating sample p2-5_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 49 regions python3 ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns Treating sample p2-9_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 57 regions python3 ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Wrote p2-all.cdt python3 ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Wrote p2-all-jtv.txt Treating sample p2-20_1 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 78 regions python3 ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns python3 ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns Treating sample p2-20_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 77 regions python3 ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Treating sample p2-20_3 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 48 regions Treating sample p2-20_4 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 65 regions 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 python3 ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Treating sample p2-20_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 64 regions python3 ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem Treating sample p2-9_2.call as male Wrote p2-9_2.vcf Wrote p2-9_2.theta2.input 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 python3 ../cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv Placed 727 variants into 19009 bins Wrote p2-9_2.nexus-ogt python3 ../cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv Wrote p2-5_5-metrics.tsv Wrote p2-5_5-segmetrics.cns with 49 regions 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 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/pdfunite 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/pdfunite Wrote p2-9_2-segmetrics.cns with 57 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 Wrote p2-9_2-metrics.tsv Treating sample p2-5_5.call as male Treating sample p2-9_2.call as male Treating sample p2-20_1.call as male Treating sample p2-20_2.call as male Treating sample p2-20_3.call as male Treating sample p2-20_4.call as male Treating sample p2-20_5.call as male Wrote p2-all.bed Wrote p2-20-metrics.tsv make[2]: Leaving directory '/<>/test' cd test && /usr/bin/make -j4 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 fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -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:217: /usr/bin/python3.8 setup.py install --root /<>/debian/cnvkit 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/python3.8 creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/metrics.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/import_rna.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/scatter.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/_version.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmetrics.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/batch.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/params.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/cnary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/reference.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/samutil.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/descriptives.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/importers.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/core.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/access.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/call.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/export.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/antitarget.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/rna.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/parallel.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/autobin.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/vary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/diagram.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/plots.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/smoothing.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/ztest.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/fix.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/hmm_learn.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/flasso.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/haar.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/hmm.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/none.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segmentation/cbs.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/reports.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/segfilters.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/commands.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/cmdutil.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/target.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/heatmap.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.8_cnvkit/build/cnvlib/coverage.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/intersect.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome creating /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/textcoord.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/gff.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/seg.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/genepred.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/vcfio.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/picard.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/vcfsimple.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/tab.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/util.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/bedio.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/tabio/seqdict.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/rangelabel.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/chromsort.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/subdivide.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/subtract.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/gary.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/combiners.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.8_cnvkit/build/skgenome/merge.py -> /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/metrics.py to metrics.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/import_rna.py to import_rna.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/scatter.py to scatter.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/_version.py to _version.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/batch.py to batch.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/params.py to params.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/cnary.py to cnary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/reference.py to reference.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/samutil.py to samutil.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/descriptives.py to descriptives.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/importers.py to importers.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/core.py to core.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/access.py to access.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/call.py to call.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/export.py to export.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/antitarget.py to antitarget.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/rna.py to rna.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/parallel.py to parallel.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/autobin.py to autobin.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/vary.py to vary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/diagram.py to diagram.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/plots.py to plots.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/smoothing.py to smoothing.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/ztest.py to ztest.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/fix.py to fix.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/hmm_learn.py to hmm_learn.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/none.py to none.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/reports.py to reports.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/segfilters.py to segfilters.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/commands.py to commands.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/target.py to target.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/heatmap.py to heatmap.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/cnvlib/coverage.py to coverage.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/intersect.py to intersect.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/gff.py to gff.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/seg.py to seg.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/picard.py to picard.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/tab.py to tab.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/util.py to util.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/chromsort.py to chromsort.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/subdivide.py to subdivide.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/subtract.py to subtract.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/gary.py to gary.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/combiners.py to combiners.cpython-38.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/skgenome/merge.py to merge.cpython-38.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' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /<>/debian/cnvkit/usr/lib/python3.8/dist-packages/CNVkit-0.9.6.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_expression_correlate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_ztest -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_annotate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-reference2targets -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-guess_baits -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-cnv_updater -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/snpfilter.sh -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.8/cnvkit-skg_convert -> /<>/debian/cnvkit/usr/bin changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-reference2targets to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-guess_baits to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 775 changing mode of /<>/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-skg_convert to 775 I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/debian/cnvkit running install running build running build_py running build_scripts running install_lib creating /<>/debian/cnvkit/usr/lib/python3.7 creating /<>/debian/cnvkit/usr/lib/python3.7/dist-packages creating /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/metrics.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/import_rna.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/scatter.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/_version.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmetrics.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/batch.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/params.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cnary.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reference.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/samutil.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/descriptives.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/importers.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/core.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/access.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/call.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/export.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/antitarget.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/rna.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/parallel.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/autobin.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/vary.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/diagram.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/plots.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/smoothing.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/ztest.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/fix.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/hmm_learn.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/flasso.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/haar.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/hmm.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/none.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segmentation/cbs.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/reports.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/segfilters.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/commands.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/cmdutil.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/target.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/heatmap.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib copying /<>/.pybuild/cpython3_3.7_cnvkit/build/cnvlib/coverage.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib creating /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/intersect.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome creating /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/textcoord.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/gff.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seg.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/genepred.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfio.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/picard.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/vcfsimple.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/tab.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/util.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/bedio.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/tabio/seqdict.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/rangelabel.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/chromsort.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subdivide.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/subtract.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/__init__.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/gary.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/combiners.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome copying /<>/.pybuild/cpython3_3.7_cnvkit/build/skgenome/merge.py -> /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/metrics.py to metrics.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/import_rna.py to import_rna.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/scatter.py to scatter.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/_version.py to _version.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmetrics.py to segmetrics.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/batch.py to batch.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/params.py to params.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cnary.py to cnary.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reference.py to reference.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/samutil.py to samutil.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/descriptives.py to descriptives.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/importers.py to importers.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/core.py to core.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/access.py to access.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/call.py to call.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/export.py to export.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/antitarget.py to antitarget.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/rna.py to rna.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/parallel.py to parallel.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/autobin.py to autobin.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/vary.py to vary.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/diagram.py to diagram.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/plots.py to plots.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/smoothing.py to smoothing.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/ztest.py to ztest.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/fix.py to fix.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/hmm_learn.py to hmm_learn.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/flasso.py to flasso.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/haar.py to haar.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/hmm.py to hmm.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/none.py to none.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segmentation/cbs.py to cbs.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/reports.py to reports.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/segfilters.py to segfilters.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/commands.py to commands.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/cmdutil.py to cmdutil.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/target.py to target.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/heatmap.py to heatmap.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/cnvlib/coverage.py to coverage.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/intersect.py to intersect.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/textcoord.py to textcoord.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/gff.py to gff.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seg.py to seg.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/genepred.py to genepred.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfio.py to vcfio.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/picard.py to picard.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/vcfsimple.py to vcfsimple.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/tab.py to tab.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/util.py to util.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/bedio.py to bedio.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/tabio/seqdict.py to seqdict.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/rangelabel.py to rangelabel.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/chromsort.py to chromsort.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subdivide.py to subdivide.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/subtract.py to subtract.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/__init__.py to __init__.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/gary.py to gary.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/combiners.py to combiners.cpython-37.pyc byte-compiling /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/skgenome/merge.py to merge.cpython-37.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' writing manifest file 'CNVkit.egg-info/SOURCES.txt' Copying CNVkit.egg-info to /<>/debian/cnvkit/usr/lib/python3.7/dist-packages/CNVkit-0.9.6.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.7/cnvkit-cnv_expression_correlate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_ztest -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_annotate -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-reference2targets -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-guess_baits -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-cnv_updater -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/snpfilter.sh -> /<>/debian/cnvkit/usr/bin copying build/scripts-3.7/cnvkit-skg_convert -> /<>/debian/cnvkit/usr/bin changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_expression_correlate to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_ztest to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_annotate to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-reference2targets to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-guess_baits to 775 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-cnv_updater to 775 changing mode of /<>/debian/cnvkit/usr/bin/snpfilter.sh to 755 changing mode of /<>/debian/cnvkit/usr/bin/cnvkit-skg_convert to 775 help2man --no-info --version-option=version \ --name="a command-line toolkit for copy number analysis." \ ./cnvkit > debian/cnvkit.1 PYTHONPATH=$PYTHONPATH:. debian/genmanpages.py 0.9.6 cd scripts && PYTHONPATH=../ help2man --no-info \ --version-string=0.9.6 --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 -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 pkgstriptranslations: processing cnvkit (in debian/cnvkit); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/cnvkit/DEBIAN/control, package cnvkit, directory debian/cnvkit pkgstripfiles: Running PNG optimization (using 4 cpus) for package cnvkit ... pkgstripfiles: No PNG files. dpkg-deb: building package 'cnvkit' in '../cnvkit_0.9.6-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../cnvkit_0.9.6-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200107-1715 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cnvkit_0.9.6-3_amd64.changes: ----------------------------- Format: 1.8 Date: Tue, 07 Jan 2020 11:48:23 +0100 Source: cnvkit Binary: cnvkit Architecture: amd64 Version: 0.9.6-3 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: cnvkit - Copy number variant detection from targeted DNA sequencing Changes: cnvkit (0.9.6-3) unstable; urgency=medium . * Don't run the autopkgtests in parallel. Checksums-Sha1: 9314230ceaddd62d0ae6d61afaef79c4053b5577 9569 cnvkit_0.9.6-3_amd64.buildinfo 43f019d33d9f6a7eb6a6acc32c724a80adaa485b 15426576 cnvkit_0.9.6-3_amd64.deb Checksums-Sha256: 091c09403d282d69943cf368a40cfc219942ab871e21f3c00cbd4f0dd5a62e12 9569 cnvkit_0.9.6-3_amd64.buildinfo 7a6456aba263be419f3e3c3d9a34c2b5429a98d9dc25c4336bb5686fd37ad67f 15426576 cnvkit_0.9.6-3_amd64.deb Files: 334ba7026611be2a16ac873d0c881c53 9569 science optional cnvkit_0.9.6-3_amd64.buildinfo 277712ea36a4b71a5a1b253b1741d807 15426576 science optional cnvkit_0.9.6-3_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cnvkit_0.9.6-3_amd64.deb ------------------------ new debian package, version 2.0. size 15426576 bytes: control archive=5928 bytes. 914 bytes, 15 lines control 16202 bytes, 185 lines md5sums 238 bytes, 12 lines * postinst #!/bin/sh 387 bytes, 12 lines * prerm #!/bin/sh Package: cnvkit Version: 0.9.6-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 69024 Depends: python3-biopython, python3-future, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate (>= 0.9.0), python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, 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. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. drwxr-xr-x root/root 0 2020-01-07 10:48 ./ drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/ drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/bin/ -rwxr-xr-x root/root 358 2020-01-07 10:48 ./usr/bin/cnvkit -rwxr-xr-x root/root 1025 2020-01-07 10:48 ./usr/bin/cnvkit-cnv_annotate -rwxr-xr-x root/root 4343 2020-01-07 10:48 ./usr/bin/cnvkit-cnv_expression_correlate -rwxr-xr-x root/root 2377 2020-01-07 10:48 ./usr/bin/cnvkit-cnv_updater -rwxr-xr-x root/root 2205 2020-01-07 10:48 ./usr/bin/cnvkit-cnv_ztest -rwxr-xr-x root/root 10278 2020-01-07 10:48 ./usr/bin/cnvkit-guess_baits -rwxr-xr-x root/root 1202 2020-01-07 10:48 ./usr/bin/cnvkit-reference2targets -rwxr-xr-x root/root 3440 2020-01-07 10:48 ./usr/bin/cnvkit-skg_convert -rwxr-xr-x root/root 1064 2019-03-21 21:03 ./usr/bin/snpfilter.sh drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/lib/ drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/lib/python3/dist-packages/CNVkit-0.9.6.egg-info/ -rw-r--r-- root/root 1218 2020-01-07 10:48 ./usr/lib/python3/dist-packages/CNVkit-0.9.6.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-01-07 10:48 ./usr/lib/python3/dist-packages/CNVkit-0.9.6.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2020-01-07 10:48 ./usr/lib/python3/dist-packages/CNVkit-0.9.6.egg-info/requires.txt -rw-r--r-- root/root 16 2020-01-07 10:48 ./usr/lib/python3/dist-packages/CNVkit-0.9.6.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-01-07 10:48 ./usr/lib/python3/dist-packages/cnvlib/ -rw-r--r-- root/root 180 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/__init__.py -rw-r--r-- root/root 22 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/_version.py -rw-r--r-- root/root 5534 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/access.py -rw-r--r-- root/root 5803 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/antitarget.py -rw-r--r-- root/root 7602 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/autobin.py -rw-r--r-- root/root 9616 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/batch.py -rw-r--r-- root/root 11809 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/call.py -rw-r--r-- root/root 3702 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/cmdutil.py -rw-r--r-- root/root 21232 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/cnary.py -rw-r--r-- root/root 87932 2020-01-07 10:48 ./usr/lib/python3/dist-packages/cnvlib/commands.py -rw-r--r-- root/root 4381 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/core.py -rw-r--r-- root/root 9056 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/coverage.py -rw-r--r-- root/root 8429 2019-03-21 21:03 ./usr/lib/python3/dist-packages/cnvlib/descriptives.py -rw-r--r-- 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+------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 157288 Build-Time: 170 Distribution: focal-proposed Host Architecture: amd64 Install-Time: 42 Job: cnvkit_0.9.6-3.dsc Machine Architecture: amd64 Package: cnvkit Package-Time: 213 Source-Version: 0.9.6-3 Space: 157288 Status: successful Version: 0.9.6-3 -------------------------------------------------------------------------------- Finished at 20200107-1715 Build needed 00:03:33, 157288k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18529078 Scanning for processes to kill in build PACKAGEBUILD-18529078