https://launchpad.net/ubuntu/+source/bcbio/1.2.4-1/+build/20201865 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-030 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:03:05 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 5 Nov 11:51:02 ntpdate[1655]: adjust time server 10.211.37.1 offset -0.000162 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20201865 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20201865 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20201865 Starting target for build PACKAGEBUILD-20201865 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20201865 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20201865 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20201865 Updating target for build PACKAGEBUILD-20201865 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1383 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [12.8 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5323 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [201 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [70.4 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [1544 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [506 kB] Fetched 22.9 MB in 8s (2742 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files base-passwd binutils binutils-common binutils-x86-64-linux-gnu cpp-10 fakeroot g++-10 gcc-10 gcc-10-base libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdebconfclient0 libfakeroot libgcc-10-dev libgcc-s1 libgomp1 libidn2-0 libip4tc2 libitm1 liblsan0 libmpc3 libncurses6 libncursesw6 libnpth0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 linux-libc-dev ncurses-base ncurses-bin systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata 64 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 229 MB of archives. After this operation, 885 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu4 [2128 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu4 [30.9 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-26.27 [1165 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-common all 1.2.6-3 [7444 B] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-dev amd64 1.2.6-3 [184 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc3 amd64 1.2.6-3 [77.2 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libcc1-0 amd64 10.2.0-16ubuntu1 [41.3 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10-base amd64 10.2.0-16ubuntu1 [19.6 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-s1 amd64 10.2.0-16ubuntu1 [41.7 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgomp1 amd64 10.2.0-16ubuntu1 [102 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libitm1 amd64 10.2.0-16ubuntu1 [26.4 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libatomic1 amd64 10.2.0-16ubuntu1 [9284 B] Get:15 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libasan6 amd64 10.2.0-16ubuntu1 [344 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 liblsan0 amd64 10.2.0-16ubuntu1 [144 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtsan0 amd64 10.2.0-16ubuntu1 [320 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libubsan1 amd64 10.2.0-16ubuntu1 [136 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libquadmath0 amd64 10.2.0-16ubuntu1 [146 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 g++-10 amd64 10.2.0-16ubuntu1 [70.1 MB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++-10-dev amd64 10.2.0-16ubuntu1 [1750 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgcc-10-dev amd64 10.2.0-16ubuntu1 [2341 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 gcc-10 amd64 10.2.0-16ubuntu1 [72.0 MB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 cpp-10 amd64 10.2.0-16ubuntu1 [63.5 MB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libstdc++6 amd64 10.2.0-16ubuntu1 [501 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.1-2ubuntu1 [48.2 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.1-2ubuntu1 [47.6 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.1-2ubuntu1 [481 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.1-2ubuntu1 [212 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.1-2ubuntu1 [3376 B] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.1-2ubuntu1 [1646 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu4 [2684 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncursesw6 amd64 6.2+20200918-1 [132 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtinfo6 amd64 6.2+20200918-1 [87.3 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-bin amd64 6.2+20200918-1 [173 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdebconfclient0 amd64 0.254ubuntu1 [6200 B] Get:40 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu4 [625 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-base all 6.2+20200918-1 [18.7 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-timesyncd amd64 246.6-2ubuntu1 [28.2 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd-sysv amd64 246.6-2ubuntu1 [10.3 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapparmor1 amd64 3.0.0-0ubuntu2 [36.3 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:48 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu2 [39.5 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-2 [52.5 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libip4tc2 amd64 1.8.5-3ubuntu3 [18.7 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main amd64 libseccomp2 amd64 2.4.3-1ubuntu5 [42.0 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 systemd amd64 246.6-2ubuntu1 [4165 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsystemd0 amd64 246.6-2ubuntu1 [273 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libudev1 amd64 246.6-2ubuntu1 [67.6 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapt-pkg6.0 amd64 2.1.11 [848 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main amd64 apt amd64 2.1.11 [1305 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build1 [69.4 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build1 [10.1 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build1 [87.2 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main amd64 tzdata all 2020d-1ubuntu1 [293 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libfakeroot amd64 1.25.3-1 [26.6 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 fakeroot amd64 1.25.3-1 [62.9 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 229 MB in 13s (18.2 MB/s) (Reading database ... 12980 files and directories currently installed.) 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Setting up libmpc3:amd64 (1.2.0-1) ... Setting up libatomic1:amd64 (10.2.0-16ubuntu1) ... Setting up libncursesw6:amd64 (6.2+20200918-1) ... Setting up libubsan1:amd64 (10.2.0-16ubuntu1) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1ubuntu1) ... Setting up libbinutils:amd64 (2.35.1-2ubuntu1) ... Setting up libc-dev-bin (2.32-0ubuntu4) ... Setting up libcc1-0:amd64 (10.2.0-16ubuntu1) ... Setting up liblsan0:amd64 (10.2.0-16ubuntu1) ... Setting up cpp-10 (10.2.0-16ubuntu1) ... Setting up libitm1:amd64 (10.2.0-16ubuntu1) ... Setting up libtsan0:amd64 (10.2.0-16ubuntu1) ... Setting up libctf0:amd64 (2.35.1-2ubuntu1) ... Setting up libtirpc3:amd64 (1.2.6-3) ... Setting up libgcc-10-dev:amd64 (10.2.0-16ubuntu1) ... Setting up libtirpc-dev:amd64 (1.2.6-3) ... Setting up libc6-dev:amd64 (2.32-0ubuntu4) ... Setting up binutils-x86-64-linux-gnu (2.35.1-2ubuntu1) ... Setting up libstdc++-10-dev:amd64 (10.2.0-16ubuntu1) ... Setting up binutils (2.35.1-2ubuntu1) ... Setting up gcc-10 (10.2.0-16ubuntu1) ... Setting up g++-10 (10.2.0-16ubuntu1) ... Setting up systemd (246.6-2ubuntu1) ... Initializing machine ID from random generator. Setting up systemd-timesyncd (246.6-2ubuntu1) ... Setting up systemd-sysv (246.6-2ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20201865 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20201865 --arch=amd64 --dist=hirsute-proposed --nolog -A bcbio_1.2.4-1.dsc Initiating build PACKAGEBUILD-20201865 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-122-generic #124-Ubuntu SMP Thu Oct 15 13:03:05 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lgw01-amd64-030.buildd +==============================================================================+ | bcbio 1.2.4-1 (amd64) Thu, 05 Nov 2020 11:52:44 +0000 | +==============================================================================+ Package: bcbio Version: 1.2.4-1 Source Version: 1.2.4-1 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20201865/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcbio_1.2.4-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bcbio-KBopOx/bcbio-1.2.4' with '<>' I: NOTICE: Log filtering will replace 'build/bcbio-KBopOx' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-mc296q/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-mc296q/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mc296q/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-mc296q/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mc296q/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-mc296q/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (142 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-mc296q/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 ... 12979 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) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-gffutils, python3-mock, python3-pandas, python3-pybedtools, python3-pysam, python3-pyvcf, python3-toolz, python3-tornado, python3-yaml, python3-scipy, python3-psutil, python3-joblib, atropos, bedtools, biobambam2, gffread, grabix, hisat2, multiqc, perl, libpicard-java, python3-biopython, python3-cyvcf2, python3-geneimpacts, python3-logbook, python3-nose, python3-requests, python3-pytest, python3-pytest-mock, bcftools, rna-star, salmon, samblaster, samtools, seqtk, tabix, tophat-recondition, wham-align, xonsh, python3-sphinx Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, python3-gffutils, python3-mock, python3-pandas, python3-pybedtools, python3-pysam, python3-pyvcf, python3-toolz, python3-tornado, python3-yaml, python3-scipy, python3-psutil, python3-joblib, atropos, bedtools, biobambam2, gffread, grabix, hisat2, multiqc, perl, libpicard-java, python3-biopython, python3-cyvcf2, python3-geneimpacts, python3-logbook, python3-nose, python3-requests, python3-pytest, python3-pytest-mock, bcftools, rna-star, salmon, samblaster, samtools, seqtk, tabix, tophat-recondition, wham-align, xonsh, python3-sphinx dpkg-deb: building package 'sbuild-build-depends-bcbio-dummy' in '/<>/resolver-mc296q/apt_archive/sbuild-build-depends-bcbio-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-bcbio-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-mc296q/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mc296q/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-mc296q/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mc296q/apt_archive ./ Sources [769 B] Get:5 copy:/<>/resolver-mc296q/apt_archive ./ Packages [823 B] Fetched 2555 B in 0s (233 kB/s) Reading package lists... Reading package lists... Install bcbio build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ant ant-optional atropos autoconf automake autopoint autotools-dev bcftools bedtools biobambam2 bsdextrautils ca-certificates-java cython3 debhelper default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fontconfig-config fonts-font-awesome fonts-lato fonts-lyx gettext gettext-base gffread grabix groff-base hisat2 intltool-debian java-common libactivation-java libaopalliance-java libapache-pom-java libarchive-zip-perl libargs4j-java libasn1-8-heimdal libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libboost-filesystem1.71.0 libboost-iostreams1.71.0 libboost-program-options1.71.0 libbrotli1 libbsd0 libcdi-api-java libcodemodel-java libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libdom4j-java libdtd-parser-java libelf1 libexpat1 libfastinfoset-java libfile-stripnondeterminism-perl libfontconfig1 libfreemarker-java libfreetype6 libgatk-native-bindings-java libgclib2 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgkl-java libgkl-jni libglib2.0-0 libgoogle-gson-java libgssapi3-heimdal libguava-java libguice-java libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhx509-5-heimdal libicu67 libimagequant0 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjemalloc2 libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoup-java libjsr305-java libkrb5-26-heimdal liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 liblightcouch-java liblog4j2-java libmagic-mgc libmagic1 libmaus2-2 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmongodb-java libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnspr4 libnss3 libpcsclite1 libpicard-java libpipeline1 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libpython3.9-minimal libpython3.9-stdlib librelaxng-datatype-java librngom-java libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsisu-guice-java libsisu-inject-java libsisu-ioc-java libsisu-plexus-java libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh-4 libstaden-read14 libstax-ex-java libstreambuffer-java libsub-override-perl libtbb2 libtiff5 libtool libtxw2-java libuchardet0 libwagon-http-java libwagon-provider-api-java libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml-commons-resolver1.1-java libxml2 libxrender1 libxsom-java libxtst6 libxz-java libyaml-0-2 m4 man-db mime-support multiqc node-jquery openjdk-11-jre-headless po-debconf python-babel-localedata python-matplotlib-data python3 python3-alabaster python3-all python3-argcomplete python3-argh python3-atomicwrites python3-attr python3-babel python3-biopython python3-certifi python3-chardet python3-click python3-colorama python3-coloredlogs python3-colormath python3-cycler python3-cyvcf2 python3-dateutil python3-decorator python3-distutils python3-docutils python3-future python3-geneimpacts python3-gffutils python3-humanfriendly python3-idna python3-imagesize python3-importlib-metadata python3-jinja2 python3-joblib python3-kiwisolver python3-lib2to3 python3-logbook python3-lzstring python3-markdown python3-markupsafe python3-matplotlib python3-minimal python3-mock python3-more-itertools python3-networkx python3-nose python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pbr python3-pil python3-pkg-resources python3-pluggy python3-ply python3-psutil python3-py python3-pybedtools python3-pyfaidx python3-pygments python3-pyparsing python3-pysam python3-pytest python3-pytest-mock python3-reportlab python3-reportlab-accel python3-requests python3-roman python3-scipy python3-setuptools python3-simplejson python3-six python3-snowballstemmer python3-spectra python3-sphinx python3-toolz python3-tornado python3-tz python3-urllib3 python3-vcf python3-wcwidth python3-yaml python3-zipp python3.8 python3.8-minimal python3.9 python3.9-minimal rna-star salmon samblaster samtools seqtk sgml-base sphinx-common sphinx-rtd-theme-common tabix tophat-recondition ttf-bitstream-vera ucf wham-align x11-common xml-core xonsh zlib1g-dev Suggested packages: ant-doc default-jdk | java-compiler | java-sdk antlr javacc junit junit4 jython libbcel-java libbsf-java libcommons-net-java libmail-java libjaxp1.3-java libjdepend-java libjsch-java liblog4j1.2-java liboro-java libregexp-java libxalan2-java autoconf-archive gnu-standards autoconf-doc texlive-latex-recommended cython-doc dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev groff libaopalliance-java-doc libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libservlet3.1-java libcommons-io-java-doc libcommons-jexl2-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java cups-common libdom4j-java-doc libmsv-java libxpp2-java libxpp3-java libdtd-parser-java-doc libjdom1-java librhino-java libgoogle-gson-java-doc libasm-java libcglib-java picard-tools libxom-java libjoptsimple-java-doc libjs-jquery-ui-docs libjsoup-java-doc libjsr305-java-doc liblcms2-utils liblog4j2-java-doc libmaven-file-management-java-doc libmaven-shared-io-java-doc libmaven-shared-utils-java-doc liblogback-java pcscd libplexus-cipher-java-doc libplexus-classworlds-java-doc libplexus-sec-dispatcher-java-doc libplexus-utils2-java-doc testng libosgi-compendium-java libosgi-core-java libtool-doc gfortran | fortran95-compiler gcj-jdk libxml-commons-resolver1.1-java-doc m4-doc apparmor less www-browser libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-renderpm python3-psycopg2 raxml t-coffee wise w3-dtd-mathml python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base python-future-doc python-jinja2-doc python-logbook-doc python-markdown-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip texlive-extra-utils texlive-latex-extra ttf-staypuft python-mock-doc python-networkx-doc python3-gdal python3-pydot python3-pygraphviz python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg python-pandas-doc python3-statsmodels python-pil-doc python3-pil-dbg python-ply-doc python-psutil-doc subversion python-pybedtools-doc python-pygments-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax python3-sphinx-rtd-theme sphinx-doc texlive-fonts-recommended texlive-plain-generic python-toolz-doc python3-pycurl python-tornado-doc python3-twisted python3.8-venv python3.8-doc binfmt-support python3.9-venv python3.9-doc cwltool sgml-base-doc tophat2 xonsh-doc Recommended packages: python3-dev curl | wget | lynx python3-hisat2 alsa-ucm-conf alsa-topology-conf dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common libjansi-java r-base-core publicsuffix libsasl2-modules libasm-java libcglib-java libltdl-dev fonts-glyphicons-halflings libjs-bootstrap libjs-jquery-tablesorter node-clipboard libjs-filesaver libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils snpeff python3-tk python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlrd python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-tables python3-olefile python3-renderpm python3-prompt-toolkit python3-setproctitle The following NEW packages will be installed: ant ant-optional atropos autoconf automake autopoint autotools-dev bcftools bedtools biobambam2 bsdextrautils ca-certificates-java cython3 debhelper default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file fontconfig-config fonts-font-awesome fonts-lato fonts-lyx gettext gettext-base gffread grabix groff-base hisat2 intltool-debian java-common libactivation-java libaopalliance-java libapache-pom-java libarchive-zip-perl libargs4j-java libasn1-8-heimdal libasound2 libasound2-data libatinject-jsr330-api-java libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libboost-filesystem1.71.0 libboost-iostreams1.71.0 libboost-program-options1.71.0 libbrotli1 libbsd0 libcdi-api-java libcodemodel-java libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libdbus-1-3 libdebhelper-perl libdeflate0 libdom4j-java libdtd-parser-java libelf1 libexpat1 libfastinfoset-java libfile-stripnondeterminism-perl libfontconfig1 libfreemarker-java libfreetype6 libgatk-native-bindings-java libgclib2 libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgkl-java libgkl-jni libglib2.0-0 libgoogle-gson-java libgssapi3-heimdal libguava-java libguice-java libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhtscodecs2 libhtsjdk-java libhttpclient-java libhttpcore-java libhx509-5-heimdal libicu67 libimagequant0 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjemalloc2 libjoptsimple-java libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjsoup-java libjsr305-java libkrb5-26-heimdal liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 liblightcouch-java liblog4j2-java libmagic-mgc libmagic1 libmaus2-2 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libmongodb-java libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnspr4 libnss3 libpcsclite1 libpicard-java libpipeline1 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python3-pygments python3-pyparsing python3-pysam python3-pytest python3-pytest-mock python3-reportlab python3-reportlab-accel python3-requests python3-roman python3-scipy python3-setuptools python3-simplejson python3-six python3-snowballstemmer python3-spectra python3-sphinx python3-toolz python3-tornado python3-tz python3-urllib3 python3-vcf python3-wcwidth python3-yaml python3-zipp python3.8 python3.8-minimal python3.9 python3.9-minimal rna-star salmon samblaster samtools sbuild-build-depends-bcbio-dummy seqtk sgml-base sphinx-common sphinx-rtd-theme-common tabix tophat-recondition ttf-bitstream-vera ucf wham-align x11-common xml-core xonsh zlib1g-dev 0 upgraded, 311 newly installed, 0 to remove and 0 not upgraded. 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hirsute/universe amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4fakesync [8616 B] Get:147 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcdi-api-java all 1.2-2 [54.5 kB] Get:148 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjaxen-java all 1.1.6-4 [214 kB] Get:149 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdom4j-java all 2.1.3-1 [309 kB] Get:150 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-io-java all 2.8.0-1 [261 kB] Get:151 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get:152 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-cli-java all 1.4-2 [55.8 kB] Get:153 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-lang3-java all 3.11-1 [526 kB] Get:154 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.7 kB] Get:155 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libaopalliance-java all 20070526-6 [9084 B] Get:156 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB] Get:157 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libguava-java all 29.0-6 [2418 kB] Get:158 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libguice-java all 4.2.3-1 [978 kB] Get:159 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven-parent-java all 31-2 [5140 B] Get:160 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get:161 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libwagon-provider-api-java all 3.3.4-1 [48.5 kB] Get:162 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven-resolver-java all 1.4.2-1 [555 kB] Get:163 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-cipher-java all 1.7-3 [15.1 kB] Get:164 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get:165 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-component-annotations-java all 2.1.0-1 [6564 B] Get:166 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get:167 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get:168 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsisu-inject-java all 0.3.3-1 [347 kB] Get:169 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsisu-plexus-java all 0.3.3-3 [182 kB] Get:170 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven3-core-java all 3.6.3-1 [1535 kB] Get:171 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get:172 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get:173 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-compress-java all 1.20-1 [556 kB] Get:174 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-io-java all 3.2.0-1 [64.9 kB] Get:175 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsnappy1v5 amd64 1.1.8-1build1 [16.7 kB] Get:176 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsnappy-jni amd64 1.1.7.7-1 [6712 B] Get:177 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsnappy-java all 1.1.7.7-1 [91.7 kB] Get:178 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxz-java all 1.8-2 [140 kB] Get:179 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get:180 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsisu-guice-java all 4.2.0-1 [785 kB] Get:181 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libsisu-ioc-java all 2.3.0-11 [492 kB] Get:182 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjsoup-java all 1.10.2-2 [337 kB] Get:183 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libwagon-http-java all 3.3.4-1 [51.1 kB] Get:184 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libistack-commons-java all 3.0.6-4 [145 kB] Get:185 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-9 [163 kB] Get:186 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-jexl2-java all 2.1.1-4 [252 kB] Get:187 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libcommons-math3-java all 3.6.1-3 [2016 kB] Get:188 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libdtd-parser-java all 1.2~svn20110404-1 [62.4 kB] Get:189 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get:190 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get:191 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libstreambuffer-java all 1.5.4-1 [71.9 kB] Get:192 http://ftpmaster.internal/ubuntu hirsute/universe amd64 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get:193 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxsom-java all 2.3.0.1-9 [396 kB] Get:194 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get:195 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libgatk-native-bindings-java all 1.0.0-2 [7260 B] Get:196 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgfortran5 amd64 10.2.0-16ubuntu1 [735 kB] Get:197 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libgkl-jni amd64 0.8.6+dfsg-1 [187 kB] Get:198 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libgkl-java amd64 0.8.6+dfsg-1 [18.0 kB] Get:199 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libhtscodecs2 amd64 0.5-3 [50.8 kB] Get:200 http://ftpmaster.internal/ubuntu hirsute/universe amd64 librngom-java all 2.3.0.1-9 [288 kB] Get:201 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtxw2-java all 2.3.0.1-9 [132 kB] Get:202 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB] Get:203 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjaxb-java all 2.3.0.1-9 [1965 kB] Get:204 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libngs-sdk2 amd64 2.10.5-1 [58.0 kB] Get:205 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libngs-sdk-dev amd64 2.10.5-1 [102 kB] Get:206 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libngs-java amd64 2.10.5-1 [76.2 kB] Get:207 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libhtsjdk-java all 2.23.0+dfsg-2 [1605 kB] Get:208 http://ftpmaster.internal/ubuntu hirsute/main amd64 libimagequant0 amd64 2.12.2-1.1 [31.4 kB] Get:209 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjemalloc2 amd64 5.2.1-1ubuntu1 [235 kB] Get:210 http://ftpmaster.internal/ubuntu hirsute/main amd64 node-jquery all 3.5.1+dfsg-4 [309 kB] Get:211 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjs-jquery all 3.5.1+dfsg-4 [2308 B] Get:212 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-7 [231 kB] Get:213 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:214 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libjs-sphinxdoc all 3.2.1-2 [122 kB] Get:215 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblapack3 amd64 3.9.0-3ubuntu1 [2152 kB] Get:216 http://ftpmaster.internal/ubuntu hirsute/universe amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get:217 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libpicard-java amd64 2.23.7+dfsg-1 [1614 kB] Get:218 http://ftpmaster.internal/ubuntu hirsute/main amd64 libpython3.9-stdlib amd64 3.9.0-5 [1752 kB] Get:219 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libstaden-read14 amd64 1.14.13-4 [230 kB] Get:220 http://ftpmaster.internal/ubuntu hirsute/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:221 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:222 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtiff5 amd64 4.1.0+git191117-2build1 [161 kB] Get:223 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwebpdemux2 amd64 0.6.1-2 [9472 B] Get:224 http://ftpmaster.internal/ubuntu hirsute/main amd64 libwebpmux3 amd64 0.6.1-2 [19.6 kB] Get:225 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-colorama all 0.4.3-1build1 [23.9 kB] Get:226 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-click all 7.1.2-1 [66.1 kB] Get:227 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-humanfriendly all 8.2-3 [68.6 kB] Get:228 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-coloredlogs all 7.3-2 [28.0 kB] Get:229 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-future all 0.18.2-4 [336 kB] Get:230 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-markupsafe amd64 1.1.1-1build1 [14.1 kB] Get:231 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-jinja2 all 2.11.2-1 [99.8 kB] Get:232 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-lzstring all 1.0.4-1 [5324 B] Get:233 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-markdown all 3.3.3-1 [66.4 kB] Get:234 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python-matplotlib-data all 3.3.2-2 [3803 kB] Get:235 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-six all 1.15.0-1 [12.0 kB] Get:236 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-dateutil all 2.8.1-4 [79.8 kB] Get:237 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-pyparsing all 2.4.7-1 [61.4 kB] Get:238 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3.9 amd64 3.9.0-5 [408 kB] Get:239 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-numpy amd64 1:1.19.4-1 [3337 kB] Get:240 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-certifi all 2020.6.20-1 [150 kB] Get:241 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-cycler all 0.10.0-3 [8132 B] Get:242 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-kiwisolver amd64 1.2.0-1build1 [284 kB] Get:243 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-pil amd64 8.0.1-1 [406 kB] Get:244 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-matplotlib amd64 3.3.2-2 [3480 kB] Get:245 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:246 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-networkx all 2.4-4ubuntu1 [855 kB] Get:247 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-chardet all 3.0.4-7 [80.2 kB] Get:248 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-idna all 2.10-1 [35.2 kB] Get:249 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-urllib3 all 1.25.9-1 [88.8 kB] Get:250 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-requests all 2.24.0+dfsg-1 [51.0 kB] Get:251 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-simplejson amd64 3.17.0-1build1 [61.9 kB] Get:252 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-colormath all 3.0.0-1 [35.2 kB] Get:253 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-spectra all 0.0.11-2 [16.4 kB] Get:254 http://ftpmaster.internal/ubuntu hirsute/universe amd64 multiqc all 1.9+dfsg-2 [514 kB] Get:255 http://ftpmaster.internal/ubuntu hirsute/main amd64 python-babel-localedata all 2.8.0+dfsg.1-4 [4985 kB] Get:256 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-all amd64 3.8.6-1 [1112 B] Get:257 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-argcomplete all 1.8.1-1.3ubuntu1 [27.2 kB] Get:258 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-atomicwrites all 1.4.0-1 [10.2 kB] Get:259 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-attr all 20.1.0-1 [40.2 kB] Get:260 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-tz all 2020.1-2 [31.6 kB] Get:261 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-babel all 2.8.0+dfsg.1-4 [84.9 kB] Get:262 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-reportlab-accel amd64 3.5.53-1 [23.3 kB] Get:263 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-reportlab all 3.5.53-1 [553 kB] Get:264 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-biopython amd64 1.78+dfsg-3build2 [1412 kB] Get:265 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-cyvcf2 amd64 0.20.9-1 [984 kB] Get:266 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-roman all 2.0.0-5 [8928 B] Get:267 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-docutils all 0.16+dfsg-3 [369 kB] Get:268 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-geneimpacts all 0.3.7-3 [33.5 kB] Get:269 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-argh all 0.26.2-1.1 [24.9 kB] Get:270 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-pyfaidx all 0.5.9.1-1 [26.4 kB] Get:271 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-gffutils all 0.10.1-2 [1028 kB] Get:272 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-imagesize all 1.2.0-2 [5868 B] Get:273 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-more-itertools all 4.2.0-3 [39.8 kB] Get:274 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-zipp all 1.0.0-3 [5440 B] Get:275 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-importlib-metadata all 1.6.0-2 [10.3 kB] Get:276 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-joblib all 0.17.0-0.1 [200 kB] Get:277 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-logbook amd64 1.5.3-4 [108 kB] Get:278 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-nose all 1.3.7-7 [116 kB] Get:279 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-packaging all 20.4-1 [27.4 kB] Get:280 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 python3-pandas-lib amd64 1.1.3+dfsg-2ubuntu3 [6279 kB] Get:281 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 python3-pandas all 1.1.3+dfsg-2ubuntu3 [2072 kB] Get:282 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-setuptools all 50.3.0-1 [451 kB] Get:283 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-pbr all 5.4.5-0ubuntu1 [64.0 kB] Get:284 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-pluggy all 0.13.0-5 [18.6 kB] Get:285 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-ply all 3.11-4 [46.6 kB] Get:286 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-psutil amd64 5.7.3-1 [155 kB] Get:287 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-py all 1.9.0-1 [71.9 kB] Get:288 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-pybedtools amd64 0.8.0-5build1 [12.2 MB] Get:289 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-pygments all 2.7.1+dfsg-1 [639 kB] Get:290 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-wcwidth all 0.1.9+dfsg1-2 [17.7 kB] Get:291 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-pytest all 4.6.11-1 [178 kB] Get:292 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-pytest-mock all 1.10.4-3 [14.6 kB] Get:293 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-snowballstemmer all 2.0.0-2 [58.3 kB] Get:294 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 sphinx-common all 3.2.1-2 [574 kB] Get:295 http://ftpmaster.internal/ubuntu hirsute/main amd64 python3-alabaster all 0.7.8-1.1 [18.6 kB] Get:296 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 python3-sphinx all 3.2.1-2 [534 kB] Get:297 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-toolz all 0.9.0-1.1 [42.1 kB] Get:298 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-tornado amd64 6.0.4-3 [280 kB] Get:299 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-vcf amd64 0.6.8+git20170215.476169c-7build1 [50.9 kB] Get:300 http://ftpmaster.internal/ubuntu hirsute/universe amd64 rna-star amd64 2.7.6a+dfsg-1 [571 kB] Get:301 http://ftpmaster.internal/ubuntu hirsute/universe amd64 libtbb2 amd64 2020.3-1 [125 kB] Get:302 http://ftpmaster.internal/ubuntu hirsute/main amd64 sphinx-rtd-theme-common all 0.5.0+dfsg-1ubuntu1 [991 kB] Get:303 http://ftpmaster.internal/ubuntu hirsute/universe amd64 salmon amd64 1.3.0+ds1-3 [1947 kB] Get:304 http://ftpmaster.internal/ubuntu hirsute/universe amd64 samblaster amd64 0.1.26-1 [26.6 kB] Get:305 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 samtools amd64 1.11-1 [516 kB] Get:306 http://ftpmaster.internal/ubuntu hirsute/universe amd64 seqtk amd64 1.3-1 [31.3 kB] Get:307 http://ftpmaster.internal/ubuntu hirsute/universe amd64 tophat-recondition all 1.4-3 [9648 B] Get:308 http://ftpmaster.internal/ubuntu hirsute/universe amd64 wham-align amd64 0.1.5-3.1 [129 kB] Get:309 http://ftpmaster.internal/ubuntu hirsute/universe amd64 xonsh all 0.9.24+dfsg-1 [332 kB] Get:310 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-mock all 4.0.2-1 [28.4 kB] Get:311 http://ftpmaster.internal/ubuntu hirsute/universe amd64 python3-scipy amd64 1.5.2-2build1 [13.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 199 MB in 13s (15.2 MB/s) Selecting previously unselected package libpython3.8-minimal:amd64. (Reading database ... 12979 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.6-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.10-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.6-1_amd64.deb ... Unpacking python3.8-minimal (3.8.6-1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.8-minimal (3.8.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13270 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.8.6-1_amd64.deb ... Unpacking python3-minimal (3.8.6-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.64ubuntu1_all.deb ... 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Setting up libwebpmux3:amd64 (0.6.1-2) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up tabix (1.11-2) ... Setting up libcdi-api-java (1.2-2) ... Setting up libelf1:amd64 (0.181-1) ... Setting up libsnappy-jni (1.1.7.7-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-2) ... Setting up sphinx-rtd-theme-common (0.5.0+dfsg-1ubuntu1) ... Setting up bedtools (2.29.2+dfsg-3build2) ... Setting up libargs4j-java (2.33-1) ... Setting up node-jquery (3.5.1+dfsg-4) ... Setting up libpython3.9-stdlib:amd64 (3.9.0-5) ... Setting up libpython3-stdlib:amd64 (3.8.6-1) ... Setting up libheimbase1-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libboost-program-options1.71.0:amd64 (1.71.0-6ubuntu10) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libdom4j-java (2.1.3-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libwagon-provider-api-java (3.3.4-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu1) ... Setting up liblapack3:amd64 (3.9.0-3ubuntu1) ... 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 (1.14-2) ... Setting up libtool (2.4.6-14) ... Setting up libgkl-java (0.8.6+dfsg-1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu2) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libwebpdemux2:amd64 (0.6.1-2) ... Setting up libasn1-8-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libmaven-parent-java (31-2) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.8-3ubuntu1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.6-1) ... Setting up libnss3:amd64 (2:3.55-1ubuntu3) ... Setting up python3-markupsafe (1.1.1-1build1) ... Setting up libhcrypto4-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-psutil (5.7.3-1) ... Setting up python3-tz (2020.1-2) ... Setting up biobambam2 (2.0.173+ds-1) ... Setting up python3-atomicwrites (1.4.0-1) ... Setting up python3-six (1.15.0-1) ... Setting up python3-simplejson (3.17.0-1build1) ... Setting up libcommons-jexl2-java (2.1.1-4) ... Setting up libmaven-resolver-java (1.4.2-1) ... Setting up python3-roman (2.0.0-5) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-jinja2 (2.11.2-1) ... Setting up tophat-recondition (1.4-3) ... Setting up python3-wcwidth (0.1.9+dfsg1-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-humanfriendly (8.2-3) ... Setting up libguava-java (29.0-6) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-snowballstemmer (2.0.0-2) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.53-1) ... Setting up python3-kiwisolver (1.2.0-1build1) ... Setting up libstreambuffer-java (1.5.4-1) ... Setting up python3-idna (2.10-1) ... Setting up cython3 (0.29.21-1ubuntu2) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up autoconf (2.69-11.1) ... Setting up python3-urllib3 (1.25.9-1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up librngom-java (2.3.0.1-9) ... Setting up dwz (0.13-5) ... Setting up hisat2 (2.2.1-1) ... Setting up groff-base (1.22.4-5) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up xml-core (0.18+nmu1) ... Setting up python3-toolz (0.9.0-1.1) ... Setting up libx11-6:amd64 (2:1.6.12-1) ... Setting up python3-dateutil (2.8.1-4) ... Setting up grabix (0.1.7-2build1) ... Setting up libtiff5:amd64 (4.1.0+git191117-2build1) ... Setting up libsnappy-java (1.1.7.7-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2ubuntu2) ... Setting up libxsom-java (2.3.0.1-9) ... Setting up libjs-jquery (3.5.1+dfsg-4) ... Setting up libcommons-codec-java (1.14-1) ... Setting up python3-argcomplete (1.8.1-1.3ubuntu1) ... Setting up python3-lib2to3 (3.8.6-1) ... Setting up python3-coloredlogs (7.3-2) ... Setting up python3-logbook (1.5.3-4) ... Setting up libavahi-client3:amd64 (0.8-3ubuntu1) ... Setting up python3.9 (3.9.0-5) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (50.3.0-1) ... Setting up automake (1:1.16.2-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.6-1) ... Setting up dh-python (4.20201102) ... Setting up python3-geneimpacts (0.3.7-3) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-pyfaidx (0.5.9.1-1) ... Setting up python3-attr (20.1.0-1) ... Setting up python3-tornado (6.0.4-3) ... Setting up python3-argh (0.26.2-1.1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up python3-setuptools (50.3.0-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up python3-py (1.9.0-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up python3-joblib (0.17.0-0.1) ... Setting up python3-babel (2.8.0+dfsg.1-4) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.3-1build1) ... Setting up python3-pbr (5.4.5-0ubuntu1) ... update-alternatives: using /usr/bin/python3-pbr to provide /usr/bin/pbr (pbr) in auto mode Setting up libcommons-io-java (2.8.0-1) ... Setting up python3-alabaster (0.7.8-1.1) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-ply (3.11-4) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up python3-all (3.8.6-1) ... Setting up python3-yaml (5.3.1-3) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-click (7.1.2-1) ... Setting up python3-networkx (2.4-4ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up man-db (2.9.3-2) ... 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 python3-nose (1.3.7-7) ... Setting up libguice-java (4.2.3-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-mock (4.0.2-1) ... Setting up python3-pil:amd64 (8.0.1-1) ... Setting up python3-pygments (2.7.1+dfsg-1) ... Setting up python3-packaging (20.4-1) ... Setting up python3-chardet (3.0.4-7) ... Setting up libjs-jquery-ui (1.12.1+dfsg-7) ... Setting up python3-requests (2.24.0+dfsg-1) ... Setting up python3-markdown (3.3.3-1) ... Setting up python3-numpy (1:1.19.4-1) ... Setting up libjs-sphinxdoc (3.2.1-2) ... Setting up python3-colormath (3.0.0-1) ... Setting up python3-reportlab (3.5.53-1) ... Setting up libcups2:amd64 (2.3.3-3ubuntu1) ... Setting up libhttpclient-java (4.5.13-1) ... Setting up liblightcouch-java (0.0.6-1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3-future (0.18.2-4) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.78+dfsg-3build2) ... Setting up python3-lzstring (1.0.4-1) ... Setting up xonsh (0.9.24+dfsg-1) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-matplotlib (3.3.2-2) ... Setting up libplexus-io-java (3.2.0-1) ... Setting up python3-scipy (1.5.2-2build1) ... Setting up python3-importlib-metadata (1.6.0-2) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up python3-spectra (0.0.11-2) ... Setting up python3-gffutils (0.10.1-2) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up liblog4j2-java (2.11.2-1) ... Setting up python3-pandas-lib:amd64 (1.1.3+dfsg-2ubuntu3) ... Setting up libsisu-inject-java (0.3.3-1) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up python3-pandas (1.1.3+dfsg-2ubuntu3) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up sphinx-common (3.2.1-2) ... Setting up python3-pluggy (0.13.0-5) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libbarclay-java (2.1.0-3) ... Setting up multiqc (1.9+dfsg-2) ... /usr/lib/python3/dist-packages/multiqc/modules/custom_content/custom_content.py:71: SyntaxWarning: "is not" with a literal. Did you mean "!="? cust_mods[c_id]['config'].update( { k:v for k, v in f.items() if k is not 'data' } ) /usr/lib/python3/dist-packages/multiqc/modules/custom_content/custom_content.py:71: SyntaxWarning: "is not" with a literal. Did you mean "!="? cust_mods[c_id]['config'].update( { k:v for k, v in f.items() if k is not 'data' } ) Setting up libmaven3-core-java (3.6.3-1) ... Setting up python3-pytest (4.6.11-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libldap-2.4-2:amd64 (2.4.53+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu4) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up python3-pytest-mock (1.10.4-3) ... Setting up libstaden-read14:amd64 (1.14.13-4) ... Setting up libhts3:amd64 (1.11-2) ... Setting up python3-pysam (0.15.4+ds-3build1) ... Setting up atropos (1.1.24+dfsg-1build1) ... Setting up bcftools (1.11-1) ... Setting up rna-star (2.7.6a+dfsg-1) ... Setting up samtools (1.11-1) ... Setting up python3-vcf (0.6.8+git20170215.476169c-7build1) ... Setting up salmon (1.3.0+ds1-3) ... Setting up python3-cyvcf2 (0.20.9-1) ... Setting up python3-pybedtools (0.8.0-5build1) ... Setting up dh-autoreconf (19) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:amd64 (11.0.9+11-0ubuntu2) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (13.2.1ubuntu1) ... Setting up ant (1.10.9-1) ... Setting up ca-certificates-java (20190405ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:GTS_Root_R2.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GTS_Root_R4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Taiwan_GRCA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Certigna.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:GTS_Root_R1.pem Adding debian:SecureTrust_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Certigna_Root_CA.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:GTS_Root_R3.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:ACCVRAIZ1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:ISRG_Root_X1.pem Adding debian:Izenpe.com.pem done. Setting up ant-optional (1.10.9-1) ... Setting up libistack-commons-java (3.0.6-4) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-9) ... Setting up libtxw2-java (2.3.0.1-9) ... Setting up libjaxb-java (2.3.0.1-9) ... Setting up libhtsjdk-java (2.23.0+dfsg-2) ... Setting up libpicard-java (2.23.7+dfsg-1) ... Processing triggers for libc-bin (2.32-0ubuntu4) ... Processing triggers for systemd (246.6-2ubuntu1) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.16+dfsg-3) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.16+dfsg-3) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (3.2.1-2) ... Setting up sbuild-build-depends-bcbio-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-122-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu2 g++-10_10.2.0-16ubuntu1 gcc-10_10.2.0-16ubuntu1 libc6-dev_2.32-0ubuntu4 libstdc++-10-dev_10.2.0-16ubuntu1 libstdc++6_10.2.0-16ubuntu1 linux-libc-dev_5.8.0-26.27 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 ant_1.10.9-1 ant-optional_1.10.9-1 apt_2.1.11 atropos_1.1.24+dfsg-1build1 autoconf_2.69-11.1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.0-6ubuntu2 bcftools_1.11-1 bedtools_2.29.2+dfsg-3build2 binutils_2.35.1-2ubuntu1 binutils-common_2.35.1-2ubuntu1 binutils-x86-64-linux-gnu_2.35.1-2ubuntu1 biobambam2_2.0.173+ds-1 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python3-importlib-metadata_1.6.0-2 python3-jinja2_2.11.2-1 python3-joblib_0.17.0-0.1 python3-kiwisolver_1.2.0-1build1 python3-lib2to3_3.8.6-1 python3-logbook_1.5.3-4 python3-lzstring_1.0.4-1 python3-markdown_3.3.3-1 python3-markupsafe_1.1.1-1build1 python3-matplotlib_3.3.2-2 python3-minimal_3.8.6-1 python3-mock_4.0.2-1 python3-more-itertools_4.2.0-3 python3-networkx_2.4-4ubuntu1 python3-nose_1.3.7-7 python3-numpy_1:1.19.4-1 python3-packaging_20.4-1 python3-pandas_1.1.3+dfsg-2ubuntu3 python3-pandas-lib_1.1.3+dfsg-2ubuntu3 python3-pbr_5.4.5-0ubuntu1 python3-pil_8.0.1-1 python3-pkg-resources_50.3.0-1 python3-pluggy_0.13.0-5 python3-ply_3.11-4 python3-psutil_5.7.3-1 python3-py_1.9.0-1 python3-pybedtools_0.8.0-5build1 python3-pyfaidx_0.5.9.1-1 python3-pygments_2.7.1+dfsg-1 python3-pyparsing_2.4.7-1 python3-pysam_0.15.4+ds-3build1 python3-pytest_4.6.11-1 python3-pytest-mock_1.10.4-3 python3-reportlab_3.5.53-1 python3-reportlab-accel_3.5.53-1 python3-requests_2.24.0+dfsg-1 python3-roman_2.0.0-5 python3-scipy_1.5.2-2build1 python3-setuptools_50.3.0-1 python3-simplejson_3.17.0-1build1 python3-six_1.15.0-1 python3-snowballstemmer_2.0.0-2 python3-spectra_0.0.11-2 python3-sphinx_3.2.1-2 python3-toolz_0.9.0-1.1 python3-tornado_6.0.4-3 python3-tz_2020.1-2 python3-urllib3_1.25.9-1 python3-vcf_0.6.8+git20170215.476169c-7build1 python3-wcwidth_0.1.9+dfsg1-2 python3-yaml_5.3.1-3 python3-zipp_1.0.0-3 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 python3.9_3.9.0-5 python3.9-minimal_3.9.0-5 readline-common_8.0-4 rna-star_2.7.6a+dfsg-1 rpcsvc-proto_1.4.2-0ubuntu4 salmon_1.3.0+ds1-3 samblaster_0.1.26-1 samtools_1.11-1 sbuild-build-depends-bcbio-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 seqtk_1.3-1 sgml-base_1.30 sphinx-common_3.2.1-2 sphinx-rtd-theme-common_0.5.0+dfsg-1ubuntu1 systemd_246.6-2ubuntu1 systemd-sysv_246.6-2ubuntu1 systemd-timesyncd_246.6-2ubuntu1 sysvinit-utils_2.96-5ubuntu1 tabix_1.11-2 tar_1.30+dfsg-7 tophat-recondition_1.4-3 ttf-bitstream-vera_1.10-8 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 ucf_3.0043 util-linux_2.36-3ubuntu1 wham-align_0.1.5-3.1 x11-common_1:7.7+19ubuntu15 xml-core_0.18+nmu1 xonsh_0.9.24+dfsg-1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Sep 25 22:59:47 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcbio_1.2.4-1.dsc dpkg-source: info: extracting bcbio in /<> dpkg-source: info: unpacking bcbio_1.2.4.orig.tar.gz dpkg-source: info: unpacking bcbio_1.2.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_tests Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20201865 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20201865 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20201865 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcbio dpkg-buildpackage: info: source version 1.2.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from bcbio-1.2.4/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean install -d /<>/debian/.debhelper/generated/_source/home pybuild --clean --test-pytest -i python{version} -p "3.9 3.8" I: pybuild base:232: python3.9 setup.py clean Traceback (most recent call last): File "/<>/setup.py", line 14, in git_run = subprocess.run(['git', 'rev-parse', '--short', 'HEAD'], stdout=subprocess.PIPE) File "/usr/lib/python3.9/subprocess.py", line 501, in run with Popen(*popenargs, **kwargs) as process: File "/usr/lib/python3.9/subprocess.py", line 947, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "/usr/lib/python3.9/subprocess.py", line 1819, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'git' E: pybuild pybuild:353: clean: plugin distutils failed with: exit code=1: python3.9 setup.py clean dh_auto_clean: error: pybuild --clean --test-pytest -i python{version} -p "3.9 3.8" returned exit code 13 make[1]: *** [debian/rules:44: override_dh_auto_clean] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: clean] Error 2 dpkg-buildpackage: error: debian/rules clean subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-11-05T11:54:35Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 1 Distribution: hirsute-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 110 Job: bcbio_1.2.4-1.dsc Machine Architecture: amd64 Package: bcbio Package-Time: 111 Source-Version: 1.2.4-1 Space: n/a Status: attempted Version: 1.2.4-1 -------------------------------------------------------------------------------- Finished at 2020-11-05T11:54:35Z Build needed 00:01:51, no disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20201865 Scanning for processes to kill in build PACKAGEBUILD-20201865