https://launchpad.net/ubuntu/+source/iva/1.0.9+ds-10/+build/19104744 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-115 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 6 Apr 20:52:40 ntpdate[11755]: adjust time server 10.211.37.1 offset -0.000732 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19104744 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 Starting target for build PACKAGEBUILD-19104744 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19104744 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 Updating target for build PACKAGEBUILD-19104744 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [757 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [171 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [826 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [502 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [6853 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5128 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [29.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [26.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/restricted Translation-en [860 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [128 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [113 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/multiverse riscv64 Packages [1140 B] Fetched 14.3 MB in 24s (596 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt coreutils cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base libapt-pkg6.0 libc-bin libc-dev-bin libc6 libc6-dev libgcc-9-dev libgnutls30 liblocale-gettext-perl libperl5.30 libstdc++-9-dev libsystemd0 libtext-charwidth-perl libtext-iconv-perl libudev1 login passwd perl-base 24 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 40.4 MB of archives. After this operation, 329 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 login riscv64 1:4.8.1-1ubuntu4 [216 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6-dev riscv64 2.31-0ubuntu7 [3659 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-dev-bin riscv64 2.31-0ubuntu7 [62.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6 riscv64 2.31-0ubuntu7 [2272 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-bin riscv64 2.31-0ubuntu7 [505 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libsystemd0 riscv64 245.2-1ubuntu3 [242 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libudev1 riscv64 245.2-1ubuntu3 [69.0 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 libapt-pkg6.0 riscv64 2.0.1ubuntu1 [797 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libgnutls30 riscv64 3.6.13-2ubuntu1 [720 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 apt riscv64 2.0.1ubuntu1 [1231 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 passwd riscv64 1:4.8.1-1ubuntu4 [752 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 g++-9 riscv64 9.3.0-10ubuntu1 [6926 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9 riscv64 9.3.0-10ubuntu1 [6788 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 libstdc++-9-dev riscv64 9.3.0-10ubuntu1 [3649 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 libgcc-9-dev riscv64 9.3.0-10ubuntu1 [404 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 cpp-9 riscv64 9.3.0-10ubuntu1 [6046 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9-base riscv64 9.3.0-10ubuntu1 [19.2 kB] Get:23 http://ftpmaster.internal/ubuntu focal/universe riscv64 gcc-8-base riscv64 8.4.0-3ubuntu2 [18.4 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 40.4 MB in 6s (6245 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../login_1%3a4.8.1-1ubuntu4_riscv64.deb ... Unpacking login (1:4.8.1-1ubuntu4) over (1:4.8.1-1ubuntu3) ... Setting up login (1:4.8.1-1ubuntu4) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu7_riscv64.deb ... Unpacking libc-dev-bin (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc6_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Setting up libc6:riscv64 (2.31-0ubuntu7) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-0ubuntu7_riscv64.deb ... Unpacking libc-bin (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Setting up libc-bin (2.31-0ubuntu7) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libsystemd0_245.2-1ubuntu3_riscv64.deb ... Unpacking libsystemd0:riscv64 (245.2-1ubuntu3) over (244.3-1ubuntu1) ... Setting up libsystemd0:riscv64 (245.2-1ubuntu3) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libudev1_245.2-1ubuntu3_riscv64.deb ... Unpacking libudev1:riscv64 (245.2-1ubuntu3) over (244.3-1ubuntu1) ... Setting up libudev1:riscv64 (245.2-1ubuntu3) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.0.1ubuntu1_riscv64.deb ... Unpacking libapt-pkg6.0:riscv64 (2.0.1ubuntu1) over (2.0.1) ... Setting up libapt-pkg6.0:riscv64 (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.13-2ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.6.13-2ubuntu1) over (3.6.11.1-2ubuntu2) ... Setting up libgnutls30:riscv64 (3.6.13-2ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_riscv64.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... 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Unpacking libgcc-9-dev:riscv64 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../6-cpp-9_9.3.0-10ubuntu1_riscv64.deb ... Unpacking cpp-9 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../7-gcc-9-base_9.3.0-10ubuntu1_riscv64.deb ... Unpacking gcc-9-base:riscv64 (9.3.0-10ubuntu1) over (9.3.0-8ubuntu1) ... Preparing to unpack .../8-gcc-8-base_8.4.0-3ubuntu2_riscv64.deb ... Unpacking gcc-8-base:riscv64 (8.4.0-3ubuntu2) over (8.4.0-3ubuntu1) ... Preparing to unpack .../9-libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up gcc-8-base:riscv64 (8.4.0-3ubuntu2) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up libc-dev-bin (2.31-0ubuntu7) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:riscv64 (9.3.0-10ubuntu1) ... Setting up libgcc-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up cpp-9 (9.3.0-10ubuntu1) ... Setting up libc6-dev:riscv64 (2.31-0ubuntu7) ... Setting up gcc-9 (9.3.0-10ubuntu1) ... Setting up libstdc++-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up g++-9 (9.3.0-10ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19104744 riscv64 focal -c chroot:build-PACKAGEBUILD-19104744 --arch=riscv64 --dist=focal --nolog iva_1.0.9+ds-10.dsc Initiating build PACKAGEBUILD-19104744 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-115 +==============================================================================+ | iva 1.0.9+ds-10 (riscv64) Mon, 06 Apr 2020 20:55:57 +0000 | +==============================================================================+ Package: iva Version: 1.0.9+ds-10 Source Version: 1.0.9+ds-10 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19104744/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/iva-8YC4Hs/resolver-3soyfY' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iva_1.0.9+ds-10.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/iva-8YC4Hs/iva-1.0.9+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-8YC4Hs' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [479 B] Get:5 copy:/<>/apt_archive ./ Packages [562 B] Fetched 1998 B in 0s (6021 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu66 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3-setuptools python3-six python3.8 python3.8-minimal samtools smalt tzdata ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl cups-common krb5-doc krb5-user liblcms2-utils pcscd libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-11-demo openjdk-11-source 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-networkx-doc python3-gdal python3-matplotlib python3-pygraphviz | python3-pydot python3-scipy python-nose-doc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pyparsing-doc python-setuptools-doc python3.8-venv python3.8-doc binfmt-support Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl alsa-ucm-conf alsa-topology-conf bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-yaml cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu66 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3-setuptools python3-six python3.8 python3.8-minimal samtools sbuild-build-depends-main-dummy smalt tzdata ucf x11-common 0 upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 221 MB of archives. After this operation, 469 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [996 B] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8-minimal riscv64 3.8.2-1ubuntu1 [698 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 openjdk-11-jre-headless riscv64 11.0.7+9-1ubuntu1 [31.1 MB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libexpat1 riscv64 2.2.9-1build1 [68.8 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 python3.8-minimal riscv64 3.8.2-1ubuntu1 [1447 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-minimal riscv64 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 libmpdec2 riscv64 2.4.2-3 [79.2 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3.8-stdlib riscv64 3.8.2-1ubuntu1 [1557 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 python3.8 riscv64 3.8.2-1ubuntu1 [364 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 libpython3-stdlib riscv64 3.8.2-0ubuntu2 [7072 B] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 python3 riscv64 3.8.2-0ubuntu2 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 gawk riscv64 1:5.0.1+dfsg-1 [381 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 libncurses6 riscv64 6.2-0ubuntu2 [86.2 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main riscv64 libdbus-1-3 riscv64 1.12.16-2ubuntu2 [161 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1122 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-pkg-resources all 45.2.0-1 [130 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-six all 1.14.0-2 [12.1 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 ucf all 3.0038+nmu1 [51.6 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5support0 riscv64 1.17-6ubuntu4 [28.3 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main riscv64 libk5crypto3 riscv64 1.17-6ubuntu4 [91.8 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main riscv64 libkeyutils1 riscv64 1.6-6ubuntu1 [9316 B] Get:38 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-3 riscv64 1.17-6ubuntu4 [295 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi-krb5-2 riscv64 1.17-6ubuntu4 [107 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 libpsl5 riscv64 0.21.0-1ubuntu1 [50.5 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main riscv64 libxau6 riscv64 1:1.0.9-0ubuntu1 [6788 B] Get:42 http://ftpmaster.internal/ubuntu focal/main riscv64 libxdmcp6 riscv64 1:1.1.3-0ubuntu1 [9952 B] Get:43 http://ftpmaster.internal/ubuntu focal/main riscv64 libxcb1 riscv64 1.14-2 [37.9 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 libx11-6 riscv64 2:1.6.9-2ubuntu1 [537 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main riscv64 libxext6 riscv64 2:1.3.4-0ubuntu1 [25.6 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main riscv64 libio-string-perl all 1.08-3 [11.1 kB] Get:53 http://ftpmaster.internal/ubuntu focal/universe riscv64 libdata-stag-perl all 0.14-2 [369 kB] Get:54 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 libbio-perl-perl all 1.7.7-1 [2567 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main riscv64 libclass-data-inheritable-perl all 0.08-3 [8084 B] Get:56 http://ftpmaster.internal/ubuntu focal/main riscv64 libdevel-stacktrace-perl all 2.0400-1 [22.7 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main riscv64 libexception-class-perl all 1.44-1 [25.9 kB] Get:58 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtest-deep-perl all 1.128-1 [41.3 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main riscv64 libcapture-tiny-perl all 0.48-1 [20.4 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main riscv64 libalgorithm-diff-perl all 1.19.03-2 [46.6 kB] Get:61 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtext-diff-perl all 1.45-1 [25.7 kB] Get:62 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtest-differences-perl all 0.67-1 [16.3 kB] Get:63 http://ftpmaster.internal/ubuntu focal/universe riscv64 libsub-uplevel-perl all 0.2800-1 [13.5 kB] Get:64 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtest-exception-perl all 0.43-1 [14.7 kB] Get:65 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtest-warn-perl all 0.36-1 [14.0 kB] Get:66 http://ftpmaster.internal/ubuntu focal/universe riscv64 libtest-most-perl all 0.35-1 [22.1 kB] Get:67 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 bioperl all 1.7.7-1 [208 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main riscv64 java-common all 0.72 [6816 B] Get:69 http://ftpmaster.internal/ubuntu focal/main riscv64 libavahi-common-data riscv64 0.7-4ubuntu6 [21.3 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main riscv64 libavahi-common3 riscv64 0.7-4ubuntu6 [18.3 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main riscv64 libavahi-client3 riscv64 0.7-4ubuntu6 [22.2 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main riscv64 libcups2 riscv64 2.3.1-9ubuntu1 [210 kB] Get:73 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 openjdk-11-jdk-headless riscv64 11.0.7+9-1ubuntu1 [145 MB] Get:74 http://ftpmaster.internal/ubuntu focal/main riscv64 liblcms2-2 riscv64 2.9-4 [127 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main riscv64 libjpeg-turbo8 riscv64 2.0.3-0ubuntu1 [101 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main riscv64 libjpeg8 riscv64 8c-2ubuntu8 [2224 B] Get:77 http://ftpmaster.internal/ubuntu focal/main riscv64 libfreetype6 riscv64 2.10.1-2 [313 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main riscv64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:79 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:80 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libfontconfig1 riscv64 2.13.1-2ubuntu3 [104 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main riscv64 libnspr4 riscv64 2:4.25-1 [91.0 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main riscv64 libnss3 riscv64 2:3.49.1-1ubuntu1 [1041 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main riscv64 libasound2-data all 1.2.2-2.1 [19.0 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main riscv64 libasound2 riscv64 1.2.2-2.1 [289 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main riscv64 libpcsclite1 riscv64 1.8.26-3 [19.5 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main riscv64 libxi6 riscv64 2:1.7.10-0ubuntu1 [27.2 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main riscv64 libxrender1 riscv64 1:0.9.10-1 [16.8 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main riscv64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main riscv64 libxtst6 riscv64 2:1.2.3-1 [11.9 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main riscv64 default-jre-headless riscv64 2:1.11-72 [3200 B] Get:91 http://ftpmaster.internal/ubuntu focal/main riscv64 ca-certificates-java all 20190405ubuntu1 [12.2 kB] Get:92 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libtool all 2.4.6-14 [161 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:94 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:97 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:99 http://ftpmaster.internal/ubuntu focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:104 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main riscv64 default-jdk-headless riscv64 2:1.11-72 [1140 B] Get:106 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-lib2to3 all 3.8.2-1ubuntu1 [74.1 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-distutils all 3.8.2-1ubuntu1 [140 kB] Get:108 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 dh-python all 4.20200315 [85.8 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main riscv64 libbrotli1 riscv64 1.0.7-6build1 [279 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main riscv64 libroken18-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [36.5 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main riscv64 libasn1-8-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [145 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimbase1-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [24.7 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main riscv64 libhcrypto4-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [86.5 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main riscv64 libwind0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [47.0 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main riscv64 libhx509-5-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [90.1 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-26-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [175 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimntlm0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [13.4 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi3-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [83.3 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-modules-db riscv64 2.1.27+dfsg-2 [13.7 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main riscv64 libsasl2-2 riscv64 2.1.27+dfsg-2 [45.2 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main riscv64 libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main riscv64 libnghttp2-14 riscv64 1.40.0-1build1 [70.9 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build1 [50.8 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main riscv64 libssh-4 riscv64 0.9.3-2ubuntu1 [147 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl3-gnutls riscv64 7.68.0-1ubuntu1 [205 kB] Get:126 http://ftpmaster.internal/ubuntu focal/universe riscv64 libdeflate0 riscv64 1.5-3 [52.1 kB] Get:127 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts3 riscv64 1.10.2-3 [328 kB] Get:128 http://ftpmaster.internal/ubuntu focal/universe riscv64 samtools riscv64 1.10-3 [486 kB] Get:129 http://ftpmaster.internal/ubuntu focal/universe riscv64 fastaq all 3.17.0-2 [47.5 kB] Get:130 http://ftpmaster.internal/ubuntu focal/universe riscv64 help2man riscv64 1.47.13 [173 kB] Get:131 http://ftpmaster.internal/ubuntu focal/universe riscv64 kmc riscv64 2.3+dfsg-7build1 [494 kB] Get:132 http://ftpmaster.internal/ubuntu focal/universe riscv64 libbambamc0 riscv64 0.0.50-3 [31.3 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main riscv64 libblas3 riscv64 3.9.0-1build1 [106 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main riscv64 libgfortran5 riscv64 10-20200324-1ubuntu1 [329 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main riscv64 liblapack3 riscv64 3.9.0-1build1 [1669 kB] Get:136 http://ftpmaster.internal/ubuntu focal/main riscv64 libssl-dev riscv64 1.1.1d-2ubuntu6 [2519 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe riscv64 mummer riscv64 3.23+dfsg-4build1 [800 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-networkx all 2.4-3ubuntu1 [855 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-nose all 1.3.7-5 [116 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-numpy riscv64 1:1.17.4-5ubuntu3 [2509 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-pyparsing all 2.4.6-1 [61.3 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-packaging all 20.3-1 [26.8 kB] Get:144 http://ftpmaster.internal/ubuntu focal/universe riscv64 python3-pysam riscv64 0.15.4+ds-1build1 [1686 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main riscv64 python3-setuptools all 45.2.0-1 [330 kB] Get:146 http://ftpmaster.internal/ubuntu focal/universe riscv64 smalt riscv64 0.7.6-9 [98.2 kB] Get:147 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libldap-2.4-2 riscv64 2.4.49+dfsg-2ubuntu1 [137 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 221 MB in 35s (6233 kB/s) Selecting previously unselected package libpython3.8-minimal:riscv64. (Reading database ... 9816 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.2.9-1build1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.2-1ubuntu1_riscv64.deb ... Unpacking python3.8-minimal (3.8.2-1ubuntu1) ... Setting up libpython3.8-minimal:riscv64 (3.8.2-1ubuntu1) ... Setting up libexpat1:riscv64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.2-1ubuntu1) ... Selecting previously unselected package python3-minimal. (Reading database ... 10107 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_riscv64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... 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Setting up liblcms2-2:riscv64 (2.9-4) ... Setting up libxau6:riscv64 (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:riscv64 (1.6-6ubuntu1) ... Setting up libpsl5:riscv64 (0.21.0-1ubuntu1) ... Setting up mime-support (3.64ubuntu1) ... Setting up java-common (0.72) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up gawk (1:5.0.1+dfsg-1) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.67-2) ... Setting up libglib2.0-0:riscv64 (2.64.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.7-6build1) ... Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:riscv64 (1.40.0-1build1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up m4 (1.4.18-4) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu1) ... Setting up libkrb5support0:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg-2) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 6 21:01:22 UTC 2020. Universal Time is now: Mon Apr 6 21:01:22 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up help2man (1.47.13) ... Setting up libasound2-data (1.2.2-2.1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfreetype6:riscv64 (2.10.1-2) ... Setting up libx11-data (2:1.6.9-2ubuntu1) ... Setting up libnspr4:riscv64 (2:4.25-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libavahi-common-data:riscv64 (0.7-4ubuntu6) ... Setting up libncurses6:riscv64 (6.2-0ubuntu2) ... Setting up libdbus-1-3:riscv64 (1.12.16-2ubuntu2) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libssl-dev:riscv64 (1.1.1d-2ubuntu6) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:riscv64 (1.8.26-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:riscv64 (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:riscv64 (2.0.3-0ubuntu1) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg-2) ... Setting up libgfortran5:riscv64 (10-20200324-1ubuntu1) ... Setting up libroken18-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libasound2:riscv64 (1.2.2-2.1) ... Setting up mummer (3.23+dfsg-4build1) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libkrb5-3:riscv64 (1.17-6ubuntu4) ... Setting up libbio-perl-perl (1.7.7-1) ... Setting up libmpdec2:riscv64 (2.4.2-3) ... Setting up libpython3.8-stdlib:riscv64 (3.8.2-1ubuntu1) ... Setting up python3.8 (3.8.2-1ubuntu1) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up kmc (2.3+dfsg-7build1) ... Setting up libpython3-stdlib:riscv64 (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libjpeg8:riscv64 (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up smalt (0.7.6-9) ... Setting up libxdmcp6:riscv64 (1:1.1.3-0ubuntu1) ... Setting up liblapack3:riscv64 (3.9.0-1build1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up libxcb1:riscv64 (1.14-2) ... Setting up libtool (2.4.6-14) ... Setting up fontconfig-config (2.13.1-2ubuntu3) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libasn1-8-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libavahi-common3:riscv64 (0.7-4ubuntu6) ... Setting up libtest-differences-perl (0.67-1) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libnss3:riscv64 (2:3.49.1-1ubuntu1) ... Setting up libexception-class-perl (1.44-1) ... Setting up libhcrypto4-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up python3-six (1.14.0-2) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up libwind0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up python3-pyparsing (2.4.6-1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... 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:riscv64 (1.17-6ubuntu4) ... Setting up libssh-4:riscv64 (0.9.3-2ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libx11-6:riscv64 (2:1.6.9-2ubuntu1) ... Setting up libfontconfig1:riscv64 (2.13.1-2ubuntu3) ... Setting up python3-lib2to3 (3.8.2-1ubuntu1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up libavahi-client3:riscv64 (0.7-4ubuntu6) ... Setting up python3-pkg-resources (45.2.0-1) ... Setting up python3-distutils (3.8.2-1ubuntu1) ... Setting up dh-python (4.20200315) ... Setting up python3-setuptools (45.2.0-1) ... Setting up libxrender1:riscv64 (1:0.9.10-1) ... Setting up libtest-most-perl (0.35-1) ... Setting up libhx509-5-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libxext6:riscv64 (2:1.3.4-0ubuntu1) ... Setting up python3-networkx (2.4-3ubuntu1) ... /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 (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-nose (1.3.7-5) ... Setting up python3-packaging (20.3-1) ... Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up python3-numpy (1:1.17.4-5ubuntu3) ... Setting up libcups2:riscv64 (2.3.1-9ubuntu1) ... Setting up libkrb5-26-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up bioperl (1.7.7-1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libxi6:riscv64 (2:1.7.10-0ubuntu1) ... Setting up libxtst6:riscv64 (2:1.2.3-1) ... Setting up libheimntlm0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgssapi3-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up libldap-2.4-2:riscv64 (2.4.49+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:riscv64 (7.68.0-1ubuntu1) ... Setting up libhts3:riscv64 (1.10.2-3) ... Setting up python3-pysam (0.15.4+ds-1build1) ... Setting up samtools (1.10-3) ... Setting up fastaq (3.17.0-2) ... Setting up default-jre-headless (2:1.11-72) ... Setting up openjdk-11-jre-headless:riscv64 (11.0.7+9-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (12.10ubuntu1) ... Setting up openjdk-11-jdk-headless:riscv64 (11.0.7+9-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-riscv64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode Setting up dh-autoreconf (19) ... Setting up default-jdk-headless (2:1.11-72) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up ca-certificates-java (20190405ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:EC-ACC.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:AffirmTrust_Premium.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Certigna.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Taiwan_GRCA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:AffirmTrust_Networking.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ACCVRAIZ1.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Secure_Global_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:SecureTrust_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Izenpe.com.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem done. Processing triggers for libc-bin (2.31-0ubuntu7) ... Processing triggers for ca-certificates (20190110ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu1 gcc-9_9.3.0-10ubuntu1 libc6-dev_2.31-0ubuntu7 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1ubuntu1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bioperl_1.7.7-1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 ca-certificates-java_20190405ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-10ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 default-jdk-headless_2:1.11-72 default-jre-headless_2:1.11-72 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 fastaq_3.17.0-2 file_1:5.38-4 findutils_4.7.0-1ubuntu1 fontconfig-config_2.13.1-2ubuntu3 fonts-dejavu-core_2.37-1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-10ubuntu1 gawk_1:5.0.1+dfsg-1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu2 gcc-9_9.3.0-10ubuntu1 gcc-9-base_9.3.0-10ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 help2man_1.47.13 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 java-common_0.72 kmc_2.3+dfsg-7build1 libacl1_2.2.53-6 libalgorithm-diff-perl_1.19.03-2 libapt-pkg6.0_2.0.1ubuntu1 libarchive-zip-perl_1.67-2 libasn1-8-heimdal_7.7.0+dfsg-1ubuntu1 libasound2_1.2.2-2.1 libasound2-data_1.2.2-2.1 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200324-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libavahi-client3_0.7-4ubuntu6 libavahi-common-data_0.7-4ubuntu6 libavahi-common3_0.7-4ubuntu6 libbambamc0_0.0.50-3 libbinutils_2.34-5ubuntu1 libbio-perl-perl_1.7.7-1 libblas3_3.9.0-1build1 libblkid1_2.34-0.1ubuntu8 libbrotli1_1.0.7-6build1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu7 libc-dev-bin_2.31-0ubuntu7 libc6_2.31-0ubuntu7 libc6-dev_2.31-0ubuntu7 libcap-ng0_0.7.9-2.1build1 libcapture-tiny-perl_0.48-1 libcc1-0_10-20200324-1ubuntu1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.45.5-2ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10ubuntu4 libcrypt1_1:4.4.10-10ubuntu4 libctf-nobfd0_2.34-5ubuntu1 libctf0_2.34-5ubuntu1 libcups2_2.3.1-9ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdbus-1-3_1.12.16-2ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.10ubuntu1 libdeflate0_1.5-3 libdevel-stacktrace-perl_2.0400-1 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libexception-class-perl_1.44-1 libexpat1_2.2.9-1build1 libext2fs2_1.45.5-2ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.6.3-2 libfontconfig1_2.13.1-2ubuntu3 libfreetype6_2.10.1-2 libgcc-9-dev_9.3.0-10ubuntu1 libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200324-1ubuntu1 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-1ubuntu1 libheimbase1-heimdal_7.7.0+dfsg-1ubuntu1 libheimntlm0-heimdal_7.7.0+dfsg-1ubuntu1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-1ubuntu1 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl22_0.22.1-1 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6-6ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1ubuntu1 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 liblapack3_3.9.0-1build1 liblcms2-2_2.9-4 libldap-2.4-2_2.4.49+dfsg-2ubuntu1 libldap-common_2.4.49+dfsg-2ubuntu1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu8 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-0ubuntu2 libncursesw6_6.2-0ubuntu2 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1build1 libnpth0_1.6-1 libnspr4_2:4.25-1 libnss3_2:3.49.1-1ubuntu1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libpcsclite1_1.8.26-3 libperl5.30_5.30.0-9build1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libpsl5_0.21.0-1ubuntu1 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.2-1ubuntu1 libpython3.8-stdlib_3.8.2-1ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-1ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu8 libsqlite3-0_3.31.1-4 libss2_1.45.5-2ubuntu1 libssh-4_0.9.3-2ubuntu1 libssl-dev_1.1.1d-2ubuntu6 libssl1.1_1.1.1d-2ubuntu6 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 libsub-override-perl_0.09-2 libsub-uplevel-perl_0.2800-1 libsystemd0_245.2-1ubuntu3 libtasn1-6_4.16.0-2 libtest-deep-perl_1.128-1 libtest-differences-perl_0.67-1 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-charwidth-perl_0.04-10 libtext-diff-perl_1.45-1 libtext-iconv-perl_1.7-7 libtinfo6_6.2-0ubuntu2 libtool_2.4.6-14 libuchardet0_0.0.6-3build1 libudev1_245.2-1ubuntu3 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu8 libwind0-heimdal_7.7.0+dfsg-1ubuntu1 libx11-6_2:1.6.9-2ubuntu1 libx11-data_2:1.6.9-2ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxi6_2:1.7.10-0ubuntu1 libxml2_2.9.10+dfsg-4build1 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-21.25 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu4 logsave_1.45.5-2ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu8 mummer_3.23+dfsg-4build1 ncurses-base_6.2-0ubuntu2 ncurses-bin_6.2-0ubuntu2 openjdk-11-jdk-headless_11.0.7+9-1ubuntu1 openjdk-11-jre-headless_11.0.7+9-1ubuntu1 openssl_1.1.1d-2ubuntu6 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu4 patch_2.7.6-6 perl_5.30.0-9build1 perl-base_5.30.0-9build1 perl-modules-5.30_5.30.0-9build1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 python3_3.8.2-0ubuntu2 python3-decorator_4.4.2-0ubuntu1 python3-distutils_3.8.2-1ubuntu1 python3-lib2to3_3.8.2-1ubuntu1 python3-minimal_3.8.2-0ubuntu2 python3-networkx_2.4-3ubuntu1 python3-nose_1.3.7-5 python3-numpy_1:1.17.4-5ubuntu3 python3-packaging_20.3-1 python3-pkg-resources_45.2.0-1 python3-pyparsing_2.4.6-1 python3-pysam_0.15.4+ds-1build1 python3-setuptools_45.2.0-1 python3-six_1.14.0-2 python3.8_3.8.2-1ubuntu1 python3.8-minimal_3.8.2-1ubuntu1 readline-common_8.0-4 samtools_1.10-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 smalt_0.7.6-9 sysvinit-utils_2.96-2.1ubuntu1 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu8 x11-common_1:7.7+19ubuntu14 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.9+ds-10 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Testsuite: autopkgtest Testsuite-Triggers: python3-packaging, trimmomatic Build-Depends: debhelper-compat (= 12), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless Package-List: iva deb science optional arch=any Checksums-Sha1: 96fdd2ca25a4c8be25942e372827020dd31098b4 8675352 iva_1.0.9+ds.orig.tar.xz 063934bc1e589ca18d4756485044136640724dc2 5556 iva_1.0.9+ds-10.debian.tar.xz Checksums-Sha256: 9d820ace5e4ad8faad1f18606f00f734e448cc1a6072ee37d8a322fca07933ca 8675352 iva_1.0.9+ds.orig.tar.xz 38358042bee249a570cc7c021208d6801d57266eb037ae9af6a068d8e69759ab 5556 iva_1.0.9+ds-10.debian.tar.xz Files: 52fb3264c946a52f53157e8760379f93 8675352 iva_1.0.9+ds.orig.tar.xz 78881e9220c9b8250dd3ec2dd7c8676f 5556 iva_1.0.9+ds-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAl4/yRIACgkQUfhKj+zK fgk5XggAgYdXtfdC2T3YTHiU4cA9Q/ihgWkUoTYLee3Aw4CdHCL0tmEg0ccytaaP 3pqHgQJJuPdf8wELpVVYRAlUjRncx6YinWujrgMpS7G2iffbpZlKtkV/64qi58nd COs7sZxE6MzOGQEPq9VseyUIlvS/j2H+Dd6XLL3leyArFHfPgbvC5ClPZbUjdVqn JRZQpn4HPat4DZQl2+GJ0RUVvuJSvr6OcLZdpZ9gZKPjfGY4EiWEEUMA/xpI8diT r5gEWYT+t4ZhjZNgMAhRaYkhVslp1chsZrpNYQSAAJfekwPndX2mOaDmlMf9HZZz jgxp+UICWCGvXNwWtQRgx0zDpQj2rw== =6aaj -----END PGP SIGNATURE----- gpgv: Signature made Sun Feb 9 08:55:46 2020 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-10.dsc dpkg-source: info: extracting iva in /<> dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.9+ds-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch 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-19104744 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19104744 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19104744 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-10 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /<>/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' chmod a-x /<>/iva/read_trim/adapters.fasta chmod a+x /<>/iva/gage/getCorrectnessStats.sh chmod a+x /<>/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /<>/iva/gage/*.java [parsing started SimpleFileObject[/<>/iva/gage/GetFastaStats.java]] [parsing completed 2171ms] [parsing started SimpleFileObject[/<>/iva/gage/SizeFasta.java]] [parsing completed 164ms] [parsing started SimpleFileObject[/<>/iva/gage/SplitFastaByLetter.java]] [parsing completed 119ms] [parsing started SimpleFileObject[/<>/iva/gage/Utils.java]] [parsing completed 491ms] [parsing started SimpleFileObject[/<>/iva/gage/getScaffoldStats.java]] [parsing completed 1089ms] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.pack/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.scripting.nashorn/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-riscv64/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [loading /modules/java.base/java/util/Iterator.class] [wrote /<>/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /<>/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /<>/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /<>/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /<>/iva/gage/Utils$Pair.class] [wrote /<>/iva/gage/Utils$Translate.class] [wrote /<>/iva/gage/Utils$ToProtein.class] [wrote /<>/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /<>/iva/gage/getScaffoldStats$Scaffold.class] [wrote /<>/iva/gage/getScaffoldStats.class] [total 132115ms] dh_auto_build -- I: pybuild base:217: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/__init__.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/kmers.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/kraken.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/egg_extract.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/contig.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/mapping.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/edge.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/seed_processor.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/assembly.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/qc.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/test_data_runner.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/graph.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/common.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/mummer.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/qc_external.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/kcount.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/seed.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/read_trim.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/external_progs.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva copying iva/contig_trim.py -> /<>/.pybuild/cpython3_3.8_iva/build/iva creating /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/.pybuild/cpython3_3.8_iva/build/iva/gage creating /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt creating /<>/.pybuild/cpython3_3.8_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/.pybuild/cpython3_3.8_iva/build/iva/read_trim creating /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.8 copying and adjusting scripts/iva_qc -> build/scripts-3.8 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.8 copying and adjusting scripts/iva -> build/scripts-3.8 changing mode of build/scripts-3.8/iva_qc from 644 to 755 changing mode of build/scripts-3.8/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.8/iva from 644 to 755 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' python3 setup.py test Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext /<>/iva/mapping.py:159: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /<>/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /<>/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /<>/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /<>/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /<>/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /<>/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /<>/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly) Test _contig_contained_in_nucmer_hits ... ok test_contig_names_size_order (assembly_test.TestAssembly) Test _contig_names_size_order ... ok test_contig_worth_extending (assembly_test.TestAssembly) Test _contig_worth_extending ... ok test_coords_to_new_contig (assembly_test.TestAssembly) Test _coords_to_new_contig ... ok test_extend_contigs_with_bam (assembly_test.TestAssembly) test _extend_contigs_with_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_contig_order_by_orfs (assembly_test.TestAssembly) Test get_contig_order_by_orfs ... ok test_get_ref_length (assembly_test.TestAssembly) Test _get_ref_length ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/assembly_test.mapped.bam' ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/assembly_test.mapped.bam' ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.bam' ok test_good_intervals_from_strand_coverage (assembly_test.TestAssembly) Test good_intervals_from_strand_coverage ... ok test_init_and_write (assembly_test.TestAssembly) test assembly initialise and write to file ... ok test_map_reads (assembly_test.TestAssembly) test _map_reads ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/assembly_test.mapped.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.assembly_test.out.bam' ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.1.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.4.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.2.5.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/tmp.filter_reads.r2j02v_f/out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/tmp.trim_strand_biased_ends.dqnskmfu/out.unsorted.bam' ok test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok test_remove_contig (assembly_test.TestAssembly) Test _remove_contig ... ok test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly) Test _remove_contig_from_nucmer_hits ... ok test_subcontigs_from_strand_bias (assembly_test.TestAssembly) Test _subcontigs_from_strand_bias ... ok test_trim_contig_for_strand_bias (assembly_test.TestAssembly) Test _trim_contig_for_strand_bias ... ok test_trim_contigs (assembly_test.TestAssembly) Test trim_contigs ... ok test_trim_strand_biased_ends (assembly_test.TestAssembly) Test _trim_strand_biased_ends ... ok test_worth_extending (assembly_test.TestAssembly) Test worth_extending ... ok test_add_left_kmer (contig_test.TestContig) Test add_left_kmer ... ok test_add_right_kmer (contig_test.TestContig) Test add_right_kmer ... ok test_extend (contig_test.TestContig) Test extend ... ok test_init (contig_test.TestContig) Test init ... ok test_len (contig_test.TestContig) Test len ... ok test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim) Test _coverage_to_trimmed_coords ... ok test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ... ok test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... ok test_change_hit_coords_with_intersection (edge_test.TestEdge) test test_change_hit_coords_with_intersection ... ok test_make_contig_first (edge_test.TestEdge) test make_contig_first ... ok test_make_contig_forwards (edge_test.TestEdge) test make_contig_forwards ... ok test_merge_into (edge_test.TestEdge) test merge_into ... ok test_open_end (edge_test.TestEdge) test open_end ... ok test_reverse (edge_test.TestEdge) test reverse ... ok test_copy_dir (egg_extract_test.TestEggExtract) test copy_dir ... ok test_copy_dir_unzipped (egg_extract_test.TestEggExtract) test copy_dir_unzipped ... ok test_copy_dir_zipped (egg_extract_test.TestEggExtract) test copy_dir_zipped ... ok test_copy_file (egg_extract_test.TestEggExtract) test copy_file ... ok test_copy_file_unzipped (egg_extract_test.TestEggExtract) test _copy_file_unzipped ... ok test_copy_file_zipped (egg_extract_test.TestEggExtract) test _copy_file_zipped ... ok test_init_and_write (egg_extract_test.TestEggExtract) test __init__ ... ok test_blastn_version (external_progs_test.TestExternalProgs) Test blastn version ... ok test_delta_filter_in_path (external_progs_test.TestExternalProgs) Test delta-filter in path ... ok test_kmc_dump_in_path (external_progs_test.TestExternalProgs) Test kmc_dump in path ... ok test_kmc_dump_version (external_progs_test.TestExternalProgs) Test kmc_dump version ... ok test_kmc_in_path (external_progs_test.TestExternalProgs) Test kmc in path ... ok test_kmc_version (external_progs_test.TestExternalProgs) Test kmc version ... ok test_makeblastdb_version (external_progs_test.TestExternalProgs) Test makeblastdb version ... ok test_nucmer_in_path (external_progs_test.TestExternalProgs) Test nucmer in path ... ok test_nucmer_version (external_progs_test.TestExternalProgs) Test nucmer version ... ok test_r_version (external_progs_test.TestExternalProgs) Test R versions ... ok test_samtools_in_path (external_progs_test.TestExternalProgs) Test samtools in path ... ok test_samtools_original_version (external_progs_test.TestExternalProgs) Test samtools original version ... ok test_samtools_version (external_progs_test.TestExternalProgs) Test samtools version ... ok test_show_coords_in_path (external_progs_test.TestExternalProgs) Test show-coords in path ... ok test_smalt_in_path (external_progs_test.TestExternalProgs) Test smalt in path ... ok test_smalt_version (external_progs_test.TestExternalProgs) Test smalt version ... ok test_add_and_get_edges (graph_test.TestGraph) test adding and getting edges ... ok test_connected_components (graph_test.TestGraph) test connected_components ... ok test_degree (graph_test.TestGraph) test degree ... ok test_edges_are_consistent (graph_test.TestGraph) test edges_are_consistent ... ok test_find_simple_path (graph_test.TestGraph) test find_simple_path ... ok test_get_nodes (graph_test.TestGraph) test get_nodes ... ok test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph) test merged_coords_from_simple_nonredundant_path ... ok test_node_to_coords (graph_test.TestGraph) test _node_to_coords ... ok test_remove_middle_node (graph_test.TestGraph) test remove_middle_node ... ok test_remove_node (graph_test.TestGraph) test remove_node ... ok test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph) test remove_redundant_nodes_from_simple_path ... ok test_simple_path_is_consistent (graph_test.TestGraph) test simple_path_is_consistent ... ok test_counts_file_to_fasta (kcount_test.TestKcount) Test _counts_file_to_fasta ... ok test_head_fastaq_fa (kcount_test.TestKcount) Test head_fastaq with FASTA input ... ok test_head_fastaq_fq (kcount_test.TestKcount) Test head_fastaq with FASTQ input ... ok test_kmc_to_kmer_counts (kcount_test.TestKcount) Test _kmc_to_kmer_counts ... ok test_median (kcount_test.TestKcount) Test _median() ... ok test_append (kmers_test.TestKmers) Test append ... ok test_commonest_kmers (kmers_test.TestKmers) ... ok test_extend (kmers_test.TestKmers) Test extend ... ok test_extension (kmers_test.TestKmers) Test extension ... ok test_init (kmers_test.TestKmers) Test __init__ ... ok test_kmer_dict (kmers_test.TestKmers) Test kmer_dict ... ok test_append_to_file (kraken_test.TestKraken) test _append_to_file ... ok test_count_cds_from_embl (kraken_test.TestKraken) test count_cds_from_embl ... ok test_genbank_to_taxon_and_gi (kraken_test.TestKraken) test _genbank_to_taxon_and_gi ... ok test_get_most_common_species_dir (kraken_test.TestKraken) Test get_most_common_species ... ok test_get_parent_taxons (kraken_test.TestKraken) test _get_parent_taxons ... ok test_load_extra_ref_info (kraken_test.TestKraken) test _load_extra_ref_info ... ok test_replace_fasta_header (kraken_test.TestKraken) test _replace_fasta_header ... ok test_species_to_dir (kraken_test.TestKraken) test species_to_dir ... ok test_bam_file_to_fasta_pair_files (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files with a region ... ok test_bam_file_to_region_fasta (mapping_test.TestMapping) Test bam_file_to_region_fasta ... ok test_bam_to_fasta (mapping_test.TestMapping) Test bam_to_fasta ... ok test_can_extend (mapping_test.TestMapping) Test can_extend ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_consensus_base (mapping_test.TestMapping) Test consensus_base ... ok test_consensus_base_both_strands (mapping_test.TestMapping) Test consensus_base_both_strands ... ok test_find_incorrect_ref_bases (mapping_test.TestMapping) Test find_incorrect_ref_bases ... ok test_get_bam_region_coverage_fwd (mapping_test.TestMapping) Test get_bam_region_coverage forward strand ... ok test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping) Test get_bam_region_coverage both strands ... ok test_get_bam_region_coverage_rev (mapping_test.TestMapping) Test get_bam_region_coverage reverse strand ... ok test_get_pair_type (mapping_test.TestMapping) Test get_pair_type ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ... ok test_map_reads_wth_flag (mapping_test.TestMapping) Test map_reads with required flag ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.flag12.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bam' ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_smalt_in_path (mapping_test.TestMapping) Test that samtools is in the user's path ... ok test_soft_clipped (mapping_test.TestMapping) Test soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.smalt.out.bam' ok test_strip_mpileup_coverage_string (mapping_test.TestMapping) Test strip_mpileup_coverage_string ... ok test_total_ref_length_from_bam (mapping_test.TestMapping) Test _total_ref_length_from_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<>/iva/tests/data/mapping_test.total_ref_length_from_bam.bam' ok test_file_read (mummer_test.TestMummer) test file_read ... ok test_is_at_ends (mummer_test.TestMummer) Test is_at_ends ... ok test_is_self_hit (mummer_test.TestMummer) Test is_self_hit ... ok test_on_same_strand (mummer_test.TestMummer) test on_same_strand ... ok test_qry_coords (mummer_test.TestMummer) Test qry_coords ... ok test_ref_coords (mummer_test.TestMummer) Test ref_coords ... ok test_run_nucmer (mummer_test.TestMummer) test run_nucmer ... ok test_sort (mummer_test.TestMummer) test sort ... ok test_swap (mummer_test.TestMummer) test swap ... ok test_to_graph_edge (mummer_test.TestMummer) Test to_graph_edge ... ok test_run_gage (qc_external_test.TestQcExternal) test run_gage ... ok test_run_ratt (qc_external_test.TestQcExternal) test run_ratt ... ok test_calculate_cds_assembly_stats (qc_test.TestQc) test _calculate_cds_assembly_stats ... ok test_calculate_contig_placement (qc_test.TestQc) test calculate_contig_placement ... ok test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc) test _calculate_ref_positions_covered_by_contigs ... ok test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ... ok test_calculate_ref_read_region_coverage (qc_test.TestQc) test _calculate_ref_read_region_coverage ... ok test_calculate_refseq_assembly_stats (qc_test.TestQc) test _calculate_refseq_assembly_stats ... ok test_calculate_should_have_assembled (qc_test.TestQc) test _calculate_should_have_assembled ... ok test_contig_placement_in_reference (qc_test.TestQc) test _contig_placement_in_reference ... ok test_contigs_and_bases_that_hit_ref (qc_test.TestQc) test _contigs_and_bases_that_hit_ref ... ok test_cov_to_R_string (qc_test.TestQc) test _cov_to_R_string ... ok test_coverage_list_to_low_cov_intervals (qc_test.TestQc) test _coverage_list_to_low_cov_intervals ... ok test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc) test _get_R_plot_contig_order_from_contig_placement ... ok test_get_contig_hits_to_reference (qc_test.TestQc) test _get_contig_hits_to_reference ... ok test_get_overlapping_qry_hits (qc_test.TestQc) test _get_overlapping_qry_hits ... ok test_get_ref_cds_from_gff (qc_test.TestQc) test _get_ref_cds_from_gff ... ok test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc) test _get_unique_and_repetitive_from_contig_hits ... ok test_gff_and_fasta_to_cds (qc_test.TestQc) test _gff_and_fasta_to_cds ... ok test_has_orf (qc_test.TestQc) test _has_orf ... ok test_hash_nucmer_hits_by_ref (qc_test.TestQc) test _hash_nucmer_hits_by_ref ... ok test_ids_in_order_from_fai (qc_test.TestQc) test _ids_in_order_from_fai ... ok test_invert_list (qc_test.TestQc) test _invert_list ... ok test_map_cds_to_assembly (qc_test.TestQc) test _map_cds_to_assembly ... ok test_mummer_coords_file_to_dict (qc_test.TestQc) test _mummer_coords_file_to_dict ... ok test_write_cds_seqs (qc_test.TestQc) test _write_cds_seqs ... ok test_write_fasta_contigs_hit_ref (qc_test.TestQc) test _write_fasta_contigs_hit_ref ... ok test_write_fasta_contigs_not_hit_ref (qc_test.TestQc) test _write_fasta_contigs_not_hit_ref ... ok test_write_ref_coverage_to_files_for_R (qc_test.TestQc) test _write_ref_coverage_to_files_for_R ... ok test_run_trimmomatic (read_trim_test.TestReadTrim) Test run_trimmomatic ... ok test_extend (seed_test.TestSeed) Test extend ... ok test_extend_with_reads_as_single_end (seed_test.TestSeed) Test _extend_with_reads_as_single_end ... ok test_extension_from_read (seed_test.TestSeed) Test _test_extension_from_read ... ok test_extensions_from_reads_file (seed_test.TestSeed) Test _extensions_from_reads_file ... ok test_init (seed_test.TestSeed) test init ... ok test_kmc_in_path (seed_test.TestSeed) Test that kmc is in the user's path ... ok test_len (seed_test.TestSeed) Test len ... ok test_write_fasta (seed_test.TestSeed) Test write_fasta ... ok ---------------------------------------------------------------------- Ran 160 tests in 161.660s OK make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install running build running build_py running build_scripts running install_lib creating /<>/debian/iva/usr creating /<>/debian/iva/usr/lib creating /<>/debian/iva/usr/lib/python3.8 creating /<>/debian/iva/usr/lib/python3.8/dist-packages creating /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/__init__.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/kmers.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/kraken.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/egg_extract.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/reads_1.fq.gz -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/reference.fasta -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_run_data/reads_2.fq.gz -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.8_iva/build/iva/contig.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/mapping.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/edge.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/seed_processor.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/assembly.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/getScaffoldStats.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/GetFastaStats.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/Utils.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/SplitFastaByLetter.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/Utils.java -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/getScaffoldStats.java -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/getCorrectnessStats.sh -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/SizeFasta.java -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/SplitFastaByLetter.java -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/Utils$ToProtein.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/Utils$Translate.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/getMummerStats.sh -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/SizeFasta.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/Utils$Pair.class -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/colsum.pl -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/gage/GetFastaStats.java -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.8_iva/build/iva/qc.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/test_data_runner.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/graph.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/common.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/mummer.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/qc_external.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/kcount.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/seed.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.8_iva/build/iva/read_trim/adapters.fasta -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.8_iva/build/iva/read_trim.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva copying /<>/.pybuild/cpython3_3.8_iva/build/iva/external_progs.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/main.ratt.pl -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/ratt.config.hiv -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/embl2gff.pl -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/start.ratt.sh -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/ratt_correction.pm -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/ratt.config -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/ratt/genbank2embl.pl -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.8_iva/build/iva/contig_trim.py -> /<>/debian/iva/usr/lib/python3.8/dist-packages/iva byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/kmers.py to kmers.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/kraken.py to kraken.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/egg_extract.py to egg_extract.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/contig.py to contig.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/mapping.py to mapping.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/edge.py to edge.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/seed_processor.py to seed_processor.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/assembly.py to assembly.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/qc.py to qc.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/graph.py to graph.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/common.py to common.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/mummer.py to mummer.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/qc_external.py to qc_external.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/kcount.py to kcount.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/seed.py to seed.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/read_trim.py to read_trim.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/external_progs.py to external_progs.cpython-38.pyc byte-compiling /<>/debian/iva/usr/lib/python3.8/dist-packages/iva/contig_trim.py to contig_trim.cpython-38.pyc running install_egg_info running egg_info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /<>/debian/iva/usr/lib/python3.8/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/iva/usr/bin copying build/scripts-3.8/iva_qc -> /<>/debian/iva/usr/bin copying build/scripts-3.8/iva_qc_make_db -> /<>/debian/iva/usr/bin copying build/scripts-3.8/iva -> /<>/debian/iva/usr/bin changing mode of /<>/debian/iva/usr/bin/iva_qc to 755 changing mode of /<>/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /<>/debian/iva/usr/bin/iva to 755 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man PYTHONPATH=. help2man -N -o /<>/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /<>/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /<>/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/<>' dh_python3 -a -O--buildsystem=pybuild dh_installinit -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 pkgstriptranslations: processing iva (in debian/iva); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/iva/DEBIAN/control, package iva, directory debian/iva pkgstripfiles: Truncating usr/share/doc/iva/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package iva ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-10_riscv64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../iva_1.0.9+ds-10_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-06T21:15:03Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.9+ds-10_riscv64.changes: -------------------------------- Format: 1.8 Date: Sun, 09 Feb 2020 09:51:06 +0100 Source: iva Binary: iva Architecture: riscv64 Version: 1.0.9+ds-10 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Changes: iva (1.0.9+ds-10) unstable; urgency=medium . * Disable tests that run KMC to circumvent failing builds on low-RAM machines. Checksums-Sha1: 70498a1121e1b68a14beade12a686208288968f3 8962 iva_1.0.9+ds-10_riscv64.buildinfo 89c1d15bd1a9de10e3d7048984b671b3bc62b5a1 8578252 iva_1.0.9+ds-10_riscv64.deb Checksums-Sha256: 1b1a2dbdd0bd5319f25748680364e03afac3f13bc8fcc107c8e48c9195f0f3f5 8962 iva_1.0.9+ds-10_riscv64.buildinfo 585a77097db29d4fdfac8e8633504181b63f51e146949a470068d7cc105672b6 8578252 iva_1.0.9+ds-10_riscv64.deb Files: b9727c242f6e251c20444f8b30ecfd81 8962 science optional iva_1.0.9+ds-10_riscv64.buildinfo 9070f8e32af0a0b8f525472e9c8a2ed5 8578252 science optional iva_1.0.9+ds-10_riscv64.deb /<>/iva_1.0.9+ds-10_riscv64.changes.new could not be renamed to /<>/iva_1.0.9+ds-10_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iva Binary: iva Architecture: riscv64 Version: 1.0.9+ds-10 Checksums-Md5: 9070f8e32af0a0b8f525472e9c8a2ed5 8578252 iva_1.0.9+ds-10_riscv64.deb Checksums-Sha1: 89c1d15bd1a9de10e3d7048984b671b3bc62b5a1 8578252 iva_1.0.9+ds-10_riscv64.deb Checksums-Sha256: 585a77097db29d4fdfac8e8633504181b63f51e146949a470068d7cc105672b6 8578252 iva_1.0.9+ds-10_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Mon, 06 Apr 2020 21:14:53 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.1-4ubuntu6), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu4), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu1), binutils (= 2.34-5ubuntu1), binutils-common (= 2.34-5ubuntu1), binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bioperl (= 1.7.7-1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), ca-certificates (= 20190110ubuntu1), ca-certificates-java (= 20190405ubuntu1), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-10ubuntu1), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), default-jdk-headless (= 2:1.11-72), default-jre-headless (= 2:1.11-72), dh-autoreconf (= 19), dh-python (= 4.20200315), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7ubuntu3), dpkg-dev (= 1.19.7ubuntu3), dwz (= 0.13-5), fastaq (= 3.17.0-2), file (= 1:5.38-4), findutils (= 4.7.0-1ubuntu1), fontconfig-config (= 2.13.1-2ubuntu3), fonts-dejavu-core (= 2.37-1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-10ubuntu1), gawk (= 1:5.0.1+dfsg-1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10-20200324-1ubuntu1), gcc-9 (= 9.3.0-10ubuntu1), gcc-9-base (= 9.3.0-10ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-4build1), gzip (= 1.10-0ubuntu4), help2man (= 1.47.13), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), java-common (= 0.72), kmc (= 2.3+dfsg-7build1), libacl1 (= 2.2.53-6), libalgorithm-diff-perl (= 1.19.03-2), libarchive-zip-perl (= 1.67-2), libasn1-8-heimdal (= 7.7.0+dfsg-1ubuntu1), libasound2 (= 1.2.2-2.1), libasound2-data (= 1.2.2-2.1), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libavahi-client3 (= 0.7-4ubuntu6), libavahi-common-data (= 0.7-4ubuntu6), libavahi-common3 (= 0.7-4ubuntu6), libbambamc0 (= 0.0.50-3), libbinutils (= 2.34-5ubuntu1), libbio-perl-perl (= 1.7.7-1), libblas3 (= 3.9.0-1build1), libblkid1 (= 2.34-0.1ubuntu8), libbrotli1 (= 1.0.7-6build1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.31-0ubuntu7), libc-dev-bin (= 2.31-0ubuntu7), libc6 (= 2.31-0ubuntu7), libc6-dev (= 2.31-0ubuntu7), libcap-ng0 (= 0.7.9-2.1build1), libcapture-tiny-perl (= 0.48-1), libcc1-0 (= 10-20200324-1ubuntu1), libclass-data-inheritable-perl (= 0.08-3), libcom-err2 (= 1.45.5-2ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libcups2 (= 2.3.1-9ubuntu1), libcurl3-gnutls (= 7.68.0-1ubuntu1), libdata-stag-perl (= 0.14-2), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdbus-1-3 (= 1.12.16-2ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdeflate0 (= 1.5-3), libdevel-stacktrace-perl (= 2.0400-1), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libexception-class-perl (= 1.44-1), libexpat1 (= 2.2.9-1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libfontconfig1 (= 2.13.1-2ubuntu3), libfreetype6 (= 2.10.1-2), libgcc-9-dev (= 9.3.0-10ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libgfortran5 (= 10-20200324-1ubuntu1), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.13-2ubuntu1), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libgssapi-krb5-2 (= 1.17-6ubuntu4), libgssapi3-heimdal (= 7.7.0+dfsg-1ubuntu1), libhcrypto4-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimbase1-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimntlm0-heimdal (= 7.7.0+dfsg-1ubuntu1), libhogweed5 (= 3.5.1+really3.5.1-2), libhts3 (= 1.10.2-3), libhx509-5-heimdal (= 7.7.0+dfsg-1ubuntu1), libicu66 (= 66.1-2ubuntu2), libidn2-0 (= 2.2.0-2), libio-string-perl (= 1.08-3), libisl22 (= 0.22.1-1), libjpeg-turbo8 (= 2.0.3-0ubuntu1), libjpeg8 (= 8c-2ubuntu8), libk5crypto3 (= 1.17-6ubuntu4), libkeyutils1 (= 1.6-6ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-1ubuntu1), libkrb5-3 (= 1.17-6ubuntu4), libkrb5support0 (= 1.17-6ubuntu4), liblapack3 (= 3.9.0-1build1), liblcms2-2 (= 2.9-4), libldap-2.4-2 (= 2.4.49+dfsg-2ubuntu1), libldap-common (= 2.4.49+dfsg-2ubuntu1), liblocale-gettext-perl (= 1.07-4), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), libmpc3 (= 1.1.0-1), libmpdec2 (= 2.4.2-3), libmpfr6 (= 4.0.2-1), libncurses6 (= 6.2-0ubuntu2), libncursesw6 (= 6.2-0ubuntu2), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.40.0-1build1), libnspr4 (= 2:4.25-1), libnss3 (= 2:3.49.1-1ubuntu1), libp11-kit0 (= 0.23.20-1build1), libpam-modules (= 1.3.1-5ubuntu4), libpam-modules-bin (= 1.3.1-5ubuntu4), libpam-runtime (= 1.3.1-5ubuntu4), libpam0g (= 1.3.1-5ubuntu4), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12build1), libpcsclite1 (= 1.8.26-3), libperl5.30 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libpng16-16 (= 1.6.37-2), libpsl5 (= 0.21.0-1ubuntu1), libpython3-stdlib (= 3.8.2-0ubuntu2), libpython3.8-minimal (= 3.8.2-1ubuntu1), libpython3.8-stdlib (= 3.8.2-1ubuntu1), libreadline8 (= 8.0-4), libroken18-heimdal (= 7.7.0+dfsg-1ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libsqlite3-0 (= 3.31.1-4), libssh-4 (= 0.9.3-2ubuntu1), libssl-dev (= 1.1.1d-2ubuntu6), libssl1.1 (= 1.1.1d-2ubuntu6), libstdc++-9-dev (= 9.3.0-10ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsub-uplevel-perl (= 0.2800-1), libsystemd0 (= 245.2-1ubuntu3), libtasn1-6 (= 4.16.0-2), libtest-deep-perl (= 1.128-1), libtest-differences-perl (= 0.67-1), libtest-exception-perl (= 0.43-1), libtest-most-perl (= 0.35-1), libtest-warn-perl (= 0.36-1), libtext-diff-perl (= 1.45-1), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-14), libuchardet0 (= 0.0.6-3build1), libudev1 (= 245.2-1ubuntu3), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libwind0-heimdal (= 7.7.0+dfsg-1ubuntu1), libx11-6 (= 2:1.6.9-2ubuntu1), libx11-data (= 2:1.6.9-2ubuntu1), libxau6 (= 1:1.0.9-0ubuntu1), libxcb1 (= 1.14-2), libxdmcp6 (= 1:1.1.3-0ubuntu1), libxext6 (= 2:1.3.4-0ubuntu1), libxi6 (= 2:1.7.10-0ubuntu1), libxml2 (= 2.9.10+dfsg-4build1), libxrender1 (= 1:0.9.10-1), libxtst6 (= 2:1.2.3-1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu4), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), mime-support (= 3.64ubuntu1), mummer (= 3.23+dfsg-4build1), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), openjdk-11-jdk-headless (= 11.0.7+9-1ubuntu1), openjdk-11-jre-headless (= 11.0.7+9-1ubuntu1), openssl (= 1.1.1d-2ubuntu6), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), python3 (= 3.8.2-0ubuntu2), python3-decorator (= 4.4.2-0ubuntu1), python3-distutils (= 3.8.2-1ubuntu1), python3-lib2to3 (= 3.8.2-1ubuntu1), python3-minimal (= 3.8.2-0ubuntu2), python3-networkx (= 2.4-3ubuntu1), python3-nose (= 1.3.7-5), python3-numpy (= 1:1.17.4-5ubuntu3), python3-packaging (= 20.3-1), python3-pkg-resources (= 45.2.0-1), python3-pyparsing (= 2.4.6-1), python3-pysam (= 0.15.4+ds-1build1), python3-setuptools (= 45.2.0-1), python3-six (= 1.14.0-2), python3.8 (= 3.8.2-1ubuntu1), python3.8-minimal (= 3.8.2-1ubuntu1), readline-common (= 8.0-4), samtools (= 1.10-3), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), smalt (= 0.7.6-9), sysvinit-utils (= 2.96-2.1ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), ucf (= 3.0038+nmu1), util-linux (= 2.34-0.1ubuntu8), x11-common (= 1:7.7+19ubuntu14), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1581238266" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iva_1.0.9+ds-10_riscv64.deb --------------------------- new Debian package, version 2.0. size 8578252 bytes: control archive=3040 bytes. 1022 bytes, 22 lines control 5477 bytes, 64 lines md5sums 231 bytes, 12 lines * postinst #!/bin/sh 380 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.9+ds-10 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8765 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/iva Description: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. drwxr-xr-x root/root 0 2020-02-09 08:51 ./ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/bin/ -rwxr-xr-x root/root 17240 2020-02-09 08:51 ./usr/bin/iva -rwxr-xr-x root/root 6228 2020-02-09 08:51 ./usr/bin/iva_qc -rwxr-xr-x root/root 2406 2020-02-09 08:51 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/ -rw-r--r-- root/root 483 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt -rw-r--r-- root/root 4 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/ -rw-r--r-- root/root 1033 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/__init__.py -rw-r--r-- root/root 28055 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/assembly.py -rw-r--r-- root/root 1856 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/common.py -rw-r--r-- root/root 1960 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig.py -rw-r--r-- root/root 4391 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig_trim.py -rw-r--r-- root/root 4903 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/edge.py -rw-r--r-- root/root 3077 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/egg_extract.py -rw-r--r-- root/root 4110 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- 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-rw-r--r-- root/root 1488 2020-01-03 11:30 ./usr/share/doc/iva/copyright drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/man/ drwxr-xr-x root/root 0 2020-02-09 08:51 ./usr/share/man/man1/ -rw-r--r-- root/root 2258 2020-02-09 08:51 ./usr/share/man/man1/iva.1.gz -rw-r--r-- root/root 1284 2020-02-09 08:51 ./usr/share/man/man1/iva_qc.1.gz -rw-r--r-- root/root 646 2020-02-09 08:51 ./usr/share/man/man1/iva_qc_make_db.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 37364 Build-Time: 618 Distribution: focal Host Architecture: riscv64 Install-Time: 502 Job: iva_1.0.9+ds-10.dsc Machine Architecture: riscv64 Package: iva Package-Time: 1146 Source-Version: 1.0.9+ds-10 Space: 37364 Status: successful Version: 1.0.9+ds-10 -------------------------------------------------------------------------------- Finished at 2020-04-06T21:15:03Z Build needed 00:19:06, 37364k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 Scanning for processes to kill in build PACKAGEBUILD-19104744 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 Stopping target for build PACKAGEBUILD-19104744 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19104744 Removing build PACKAGEBUILD-19104744