Sat Dec 4 16:24:22 UTC 2021 I: starting to build iva/buster/amd64 on jenkins on '2021-12-04 16:24' Sat Dec 4 16:24:22 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_28/98195/console.log Sat Dec 4 16:24:22 UTC 2021 I: Downloading source for buster/iva=1.0.9+ds-6 --2021-12-04 16:24:22-- http://deb.debian.org/debian/pool/main/i/iva/iva_1.0.9%2bds-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1890 (1.8K) Saving to: ‘iva_1.0.9+ds-6.dsc’ 0K . 100% 124M=0s 2021-12-04 16:24:23 (124 MB/s) - ‘iva_1.0.9+ds-6.dsc’ saved [1890/1890] Sat Dec 4 16:24:23 UTC 2021 I: iva_1.0.9+ds-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.9+ds-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Testsuite: autopkgtest Testsuite-Triggers: trimmomatic Build-Depends: debhelper (>= 11~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, 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 a0309bf709286986b8968f148c62ce30486978ff 4276 iva_1.0.9+ds-6.debian.tar.xz Checksums-Sha256: 9d820ace5e4ad8faad1f18606f00f734e448cc1a6072ee37d8a322fca07933ca 8675352 iva_1.0.9+ds.orig.tar.xz f2abbb94904751272afd66734e61b0111ffac55a75db0eaa4449ca71fcf27168 4276 iva_1.0.9+ds-6.debian.tar.xz Files: 52fb3264c946a52f53157e8760379f93 8675352 iva_1.0.9+ds.orig.tar.xz 02f2a458b5e60db7f16d058af4a7a44f 4276 iva_1.0.9+ds-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQFFBAEBCgAvFiEEhFH5F4Fy5+Lcc/eVUfhKj+zKfgkFAltiD50RHHNhdHRhQGRl Ymlhbi5vcmcACgkQUfhKj+zKfgljJwf+K/sHY5TlRBcS19KKQPvadEQDgk2E6vKV xkDtUuSwqQ10WtoQB+9iDY+wNuvGQjEkjvOHgne98MLDj2KjVGYb5GEtC5vnH2l8 zWcls7vpLUSqeYAcKNGB8r6y0q8o05nxMhZgkZ4spsbGDCxKD9QYsjTMtHae0CdR SEMtnZtGKXC2QBmPPupafaOs09/MkXg/wzNdmijKCW/vK6urhvzx8HV3ba2kAG+K SQ7CBp5QdFnJGXoJ/5oRpCUi9H0Ca7ejxVOBp13hVMY9jfwqMdDoNzGEaJcApBl8 wEfy8IMSQLButTWcnbISJB2lt61QQRWTTT67glkhv5s1lO+6B3DI/g== =F9eJ -----END PGP SIGNATURE----- Sat Dec 4 16:24:23 UTC 2021 I: Checking whether the package is not for us Sat Dec 4 16:24:23 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sat Dec 4 16:24:23 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sat Dec 4 16:26:03 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 6 10:47:25 -12 2023 I: pbuilder-time-stamp: 1673045245 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.9+ds-6.dsc] I: copying [./iva_1.0.9+ds.orig.tar.xz] I: copying [./iva_1.0.9+ds-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Aug 1 07:53:01 2018 -12 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: issuer "satta@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-6.dsc dpkg-source: info: extracting iva in iva-1.0.9+ds dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.9+ds-6.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3825331/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='7c2f7f01960e473fbe8d934864e64381' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3825331' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/pbuilderrc_CxXK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/b1 --logfile b1/build.log iva_1.0.9+ds-6.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/3825331/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 1.6); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on kmc; however: Package kmc is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on smalt; however: Package smalt is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk-headless{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} java-common{a} kmc{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbambamc0{a} libbio-perl-perl{a} libblas3{a} libbsd0{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcroco3{a} libcups2{a} libcurl3-gnutls{a} libdata-stag-perl{a} libdbus-1-3{a} libdeflate0{a} libdevel-stacktrace-perl{a} libelf1{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts2{a} libicu63{a} libio-string-perl{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} mummer{a} openjdk-11-jdk-headless{a} openjdk-11-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-decorator{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-networkx{a} python3-nose{a} python3-numpy{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.7{a} python3.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} smalt{a} ucf{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl cwltool dbus krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix python python3-gdal python3-scipy python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 129 newly installed, 0 to remove and 0 not upgraded. Need to get 312 MB of archives. After unpacking 594 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libbio-perl-perl all 1.7.2-3 [4553 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 38 http://deb.debian.org/debian buster/main amd64 libdevel-stacktrace-perl all 2.0300-1 [28.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libexception-class-perl all 1.44-1 [32.3 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libtest-deep-perl all 1.128-1 [48.8 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libalgorithm-diff-perl all 1.19.03-2 [47.9 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libtext-diff-perl all 1.45-1 [27.7 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libtest-differences-perl all 0.65-1 [18.1 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libsub-uplevel-perl all 0.2800-1 [16.3 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libtest-warn-perl all 0.36-1 [16.2 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 bioperl all 1.7.2-3 [418 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2~deb10u1 [37.2 MB] Get: 79 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 openjdk-11-jdk-headless amd64 11.0.12+7-2~deb10u1 [221 MB] Get: 97 http://deb.debian.org/debian buster/main amd64 default-jdk-headless amd64 2:1.11-71 [1104 B] Get: 98 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 fastaq all 3.17.0-2 [47.8 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 kmc amd64 2.3+dfsg-7 [466 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libbambamc0 amd64 0.0.50-3 [37.9 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 libssl-dev amd64 1.1.1d-0+deb10u7 [1795 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 python3-decorator all 4.3.0-1.1 [14.5 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 python3-networkx all 2.2-1 [818 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 python3-nose all 1.3.7-4 [132 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 smalt amd64 0.7.6-8 [113 kB] Fetched 312 MB in 5s (68.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../2-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../3-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../4-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../5-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../6-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../7-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../8-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package gawk. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19862 files and directories currently installed.) Preparing to unpack .../0-gawk_1%3a4.2.1+dfsg-1_amd64.deb ... Unpacking gawk (1:4.2.1+dfsg-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../1-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../2-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../3-libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../4-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../5-python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20307 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../2-libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../3-libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../4-python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../5-libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20744 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package ucf. Preparing to unpack .../006-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../007-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../008-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../009-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../010-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../011-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../012-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../013-libdata-stag-perl_0.14-2_all.deb ... Unpacking libdata-stag-perl (0.14-2) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../014-libbio-perl-perl_1.7.2-3_all.deb ... Unpacking libbio-perl-perl (1.7.2-3) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../015-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../016-libdevel-stacktrace-perl_2.0300-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0300-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../017-libexception-class-perl_1.44-1_all.deb ... Unpacking libexception-class-perl (1.44-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../018-libtest-deep-perl_1.128-1_all.deb ... Unpacking libtest-deep-perl (1.128-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../019-libcapture-tiny-perl_0.48-1_all.deb ... Unpacking libcapture-tiny-perl (0.48-1) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../020-libalgorithm-diff-perl_1.19.03-2_all.deb ... Unpacking libalgorithm-diff-perl (1.19.03-2) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../021-libtext-diff-perl_1.45-1_all.deb ... Unpacking libtext-diff-perl (1.45-1) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../022-libtest-differences-perl_0.65-1_all.deb ... Unpacking libtest-differences-perl (0.65-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../023-libsub-uplevel-perl_0.2800-1_all.deb ... Unpacking libsub-uplevel-perl (0.2800-1) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../024-libtest-exception-perl_0.43-1_all.deb ... Unpacking libtest-exception-perl (0.43-1) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../025-libtest-warn-perl_0.36-1_all.deb ... Unpacking libtest-warn-perl (0.36-1) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../026-libtest-most-perl_0.35-1_all.deb ... Unpacking libtest-most-perl (0.35-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../027-bioperl_1.7.2-3_all.deb ... Unpacking bioperl (1.7.2-3) ... Selecting previously unselected package openssl. Preparing to unpack .../028-openssl_1.1.1d-0+deb10u7_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u7) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../029-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package java-common. Preparing to unpack .../030-java-common_0.71_all.deb ... Unpacking java-common (0.71) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../031-libavahi-common-data_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../032-libavahi-common3_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-common3:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../033-libdbus-1-3_1.12.20-0+deb10u1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../034-libavahi-client3_0.7-4+deb10u1_amd64.deb ... Unpacking libavahi-client3:amd64 (0.7-4+deb10u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../035-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../036-libkrb5support0_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../037-libk5crypto3_1.17-3+deb10u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../038-libkrb5-3_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../039-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../040-libcups2_2.2.10-6+deb10u4_amd64.deb ... Unpacking libcups2:amd64 (2.2.10-6+deb10u4) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../041-liblcms2-2_2.9-3_amd64.deb ... Unpacking liblcms2-2:amd64 (2.9-3) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../042-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../043-libpng16-16_1.6.36-6_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../044-libfreetype6_2.9.1-3+deb10u2_amd64.deb ... Unpacking libfreetype6:amd64 (2.9.1-3+deb10u2) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../045-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../046-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../047-libfontconfig1_2.13.1-2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../048-libnspr4_2%3a4.20-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.20-1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../049-libnss3_2%3a3.42.1-1+deb10u3_amd64.deb ... Unpacking libnss3:amd64 (2:3.42.1-1+deb10u3) ... Selecting previously unselected package libasound2-data. Preparing to unpack .../050-libasound2-data_1.1.8-1_all.deb ... Unpacking libasound2-data (1.1.8-1) ... Selecting previously unselected package libasound2:amd64. Preparing to unpack .../051-libasound2_1.1.8-1_amd64.deb ... Unpacking libasound2:amd64 (1.1.8-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../052-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../053-libgraphite2-3_1.3.13-7_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.13-7) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../054-libharfbuzz0b_2.3.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (2.3.1-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../055-libpcsclite1_1.8.24-1_amd64.deb ... Unpacking libpcsclite1:amd64 (1.8.24-1) ... Selecting previously unselected package openjdk-11-jre-headless:amd64. Preparing to unpack .../056-openjdk-11-jre-headless_11.0.12+7-2~deb10u1_amd64.deb ... Unpacking openjdk-11-jre-headless:amd64 (11.0.12+7-2~deb10u1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../057-default-jre-headless_2%3a1.11-71_amd64.deb ... Unpacking default-jre-headless (2:1.11-71) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../058-ca-certificates-java_20190405_all.deb ... Unpacking ca-certificates-java (20190405) ... Selecting previously unselected package libtool. Preparing to unpack .../059-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../060-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../061-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../062-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../063-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../064-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../065-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../066-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../067-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../068-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../069-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../070-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../071-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../072-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../073-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package openjdk-11-jdk-headless:amd64. Preparing to unpack .../074-openjdk-11-jdk-headless_11.0.12+7-2~deb10u1_amd64.deb ... Unpacking openjdk-11-jdk-headless:amd64 (11.0.12+7-2~deb10u1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../075-default-jdk-headless_2%3a1.11-71_amd64.deb ... Unpacking default-jdk-headless (2:1.11-71) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../076-python3-lib2to3_3.7.3-1_all.deb ... Unpacking python3-lib2to3 (3.7.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../077-python3-distutils_3.7.3-1_all.deb ... Unpacking python3-distutils (3.7.3-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../078-dh-python_3.20190308_all.deb ... Unpacking dh-python (3.20190308) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../079-python3-pkg-resources_40.8.0-1_all.deb ... Unpacking python3-pkg-resources (40.8.0-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../080-libsasl2-modules-db_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../081-libsasl2-2_2.1.27+dfsg-1+deb10u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../082-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../083-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../084-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../085-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../086-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../087-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../088-libcurl3-gnutls_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../089-libdeflate0_1.2-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.2-1) ... Selecting previously unselected package libhts2:amd64. Preparing to unpack .../090-libhts2_1.9-12~deb10u1_amd64.deb ... Unpacking libhts2:amd64 (1.9-12~deb10u1) ... Selecting previously unselected package samtools. Preparing to unpack .../091-samtools_1.9-4_amd64.deb ... Unpacking samtools (1.9-4) ... Selecting previously unselected package fastaq. Preparing to unpack .../092-fastaq_3.17.0-2_all.deb ... Unpacking fastaq (3.17.0-2) ... Selecting previously unselected package help2man. Preparing to unpack .../093-help2man_1.47.8_amd64.deb ... Unpacking help2man (1.47.8) ... Selecting previously unselected package kmc. Preparing to unpack .../094-kmc_2.3+dfsg-7_amd64.deb ... Unpacking kmc (2.3+dfsg-7) ... Selecting previously unselected package libbambamc0. Preparing to unpack .../095-libbambamc0_0.0.50-3_amd64.deb ... Unpacking libbambamc0 (0.0.50-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../096-libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../097-libblas3_3.8.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.8.0-2) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../098-liblapack3_3.8.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.8.0-2) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../099-libssl-dev_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl-dev:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package mummer. Preparing to unpack .../100-mummer_3.23+dfsg-4_amd64.deb ... Unpacking mummer (3.23+dfsg-4) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../101-python3-decorator_4.3.0-1.1_all.deb ... Unpacking python3-decorator (4.3.0-1.1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../102-python3-networkx_2.2-1_all.deb ... Unpacking python3-networkx (2.2-1) ... Selecting previously unselected package python3-nose. Preparing to unpack .../103-python3-nose_1.3.7-4_all.deb ... Unpacking python3-nose (1.3.7-4) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../104-python3-numpy_1%3a1.16.2-1_amd64.deb ... Unpacking python3-numpy (1:1.16.2-1) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../105-python3-pysam_0.15.2+ds-2_amd64.deb ... Unpacking python3-pysam (0.15.2+ds-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../106-python3-setuptools_40.8.0-1_all.deb ... Unpacking python3-setuptools (40.8.0-1) ... Selecting previously unselected package smalt. Preparing to unpack .../107-smalt_0.7.6-8_amd64.deb ... Unpacking smalt (0.7.6-8) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up java-common (0.71) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up gawk (1:4.2.1+dfsg-1) ... Setting up libalgorithm-diff-perl (1.19.03-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up m4 (1.4.18-2) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libasound2-data (1.1.8-1) ... Setting up libio-string-perl (1.08-3) ... Setting up autotools-dev (20180224.1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libavahi-common-data:amd64 (0.7-4+deb10u1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libssl-dev:amd64 (1.1.1d-0+deb10u7) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up autoconf (2.69-11) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libasound2:amd64 (1.1.8-1) ... Setting up mummer (3.23+dfsg-4) ... Setting up libsub-uplevel-perl (0.2800-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libdevel-stacktrace-perl (2.0300-1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libbio-perl-perl (1.7.2-3) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up kmc (2.3+dfsg-7) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up smalt (0.7.6-8) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libtool (2.4.6-9) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libavahi-common3:amd64 (0.7-4+deb10u1) ... Setting up libtest-differences-perl (0.65-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up libexception-class-perl (1.44-1) ... Setting up help2man (1.47.8) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libtest-exception-perl (0.43-1) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libtest-most-perl (0.35-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up libcups2:amd64 (2.2.10-6+deb10u4) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up bioperl (1.7.2-3) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up python3-networkx (2.2-1) ... Setting up python3-nose (1.3.7-4) ... Setting up samtools (1.9-4) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up fastaq (3.17.0-2) ... Setting up dh-autoreconf (19) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre-headless:amd64 (11.0.12+7-2~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up debhelper (12.1.1) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.12+7-2~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.11-71) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/iva-1.0.9+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iva_1.0.9+ds-6_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iva-1.0.9+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /build/iva-1.0.9+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/iva-1.0.9+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.7 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 '/build/iva-1.0.9+ds' chmod a-x /build/iva-1.0.9+ds/iva/read_trim/adapters.fasta chmod a+x /build/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh chmod a+x /build/iva-1.0.9+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /build/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] [parsing completed 76ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/Utils.java]] [parsing completed 9ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] [parsing completed 13ms] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.scripting.nashorn/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.aot/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/jdk.naming.ldap/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.pack/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/java.smartcardio/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-amd64/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 /build/iva-1.0.9+ds/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$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /build/iva-1.0.9+ds/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /build/iva-1.0.9+ds/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /build/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$Pair.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$Translate.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class] [wrote /build/iva-1.0.9+ds/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats.class] [total 1407ms] 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 /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/test_data_runner.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/seed_processor.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/seed.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/read_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/qc_external.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/qc.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/mummer.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/mapping.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kraken.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kmers.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/kcount.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/graph.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/external_progs.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/egg_extract.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/edge.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/contig_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/contig.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/common.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/assembly.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva copying iva/__init__.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/Utils.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.7 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.7 copying and adjusting scripts/iva_qc -> build/scripts-3.7 copying and adjusting scripts/iva -> build/scripts-3.7 changing mode of build/scripts-3.7/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.7/iva_qc from 644 to 755 changing mode of build/scripts-3.7/iva from 644 to 755 make[1]: Leaving directory '/build/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iva-1.0.9+ds' 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 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 /usr/lib/python3/dist-packages/pysam/__init__.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working import pysam.libcsamfile as libcsamfile /build/iva-1.0.9+ds/iva/mapping.py:157: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /build/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /build/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /build/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /build/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /build/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /usr/lib/python3/dist-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Mapping, Set, Iterable /build/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /build/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') test_add_new_seed_contig (assembly_test.TestAssembly) Test add_new_seed_contig ... ok 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 ... 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 ... ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... 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 ... ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... 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_get_most_common_kmers (kcount_test.TestKcount) Test get_most_common_kmers ... 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_run_kmc (kcount_test.TestKcount) Test test_run_kmc ... ok test_run_kmc_two_threads (kcount_test.TestKcount) Test test_run_kmc with two threads ... 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 ... 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 ... 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 ... ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... 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 ... ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... 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 ... 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 ... 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 164 tests in 6.725s OK make[1]: Leaving directory '/build/iva-1.0.9+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/iva-1.0.9+ds/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 /build/iva-1.0.9+ds/debian/iva/usr creating /build/iva-1.0.9+ds/debian/iva/usr/lib creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7 creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_run_data creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt.config -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/ratt creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/Utils.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/__init__.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/assembly.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/common.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/contig.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/contig_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/edge.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/egg_extract.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/external_progs.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/graph.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kcount.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kmers.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/kraken.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/mapping.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/mummer.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/qc.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/qc_external.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/read_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/seed.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/seed_processor.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.7_iva/build/iva/test_data_runner.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/__init__.py to __init__.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/assembly.py to assembly.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/common.py to common.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/contig.py to contig.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/contig_trim.py to contig_trim.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/edge.py to edge.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/egg_extract.py to egg_extract.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/external_progs.py to external_progs.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/graph.py to graph.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kcount.py to kcount.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kmers.py to kmers.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/kraken.py to kraken.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/mapping.py to mapping.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/mummer.py to mummer.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/qc.py to qc.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/qc_external.py to qc_external.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/read_trim.py to read_trim.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/seed.py to seed.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/seed_processor.py to seed_processor.cpython-37.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-37.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 /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.7/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.7/iva -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.7/iva_qc -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.7/iva_qc_make_db -> /build/iva-1.0.9+ds/debian/iva/usr/bin changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva to 755 changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755 changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/iva-1.0.9+ds' mkdir -p /build/iva-1.0.9+ds/debian/man PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /build/iva-1.0.9+ds/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 '/build/iva-1.0.9+ds' dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package iva: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-6_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iva_1.0.9+ds-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3825331 and its subdirectories I: Current time: Fri Jan 6 10:49:04 -12 2023 I: pbuilder-time-stamp: 1673045344 Sat Dec 4 16:26:04 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Sat Dec 4 16:26:04 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Sat Dec 4 16:29:04 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Sat Dec 4 16:29:05 UTC 2021 I: iva_1.0.9+ds-6_amd64.changes: Format: 1.8 Date: Wed, 01 Aug 2018 21:19:30 +0200 Source: iva Binary: iva Architecture: amd64 Version: 1.0.9+ds-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Changes: iva (1.0.9+ds-6) unstable; urgency=medium . * Use correct Vcs-Git URL. * Remove ancient X-Python3-Version field. * Use Debian's Perl path in RATT scripts. Checksums-Sha1: e3031334036e1fa8cb71f033ec1c5cb5888478cd 7748 iva_1.0.9+ds-6_amd64.buildinfo d90fbd993e73705b096ebbbe5b5a17fd7fb43243 8578168 iva_1.0.9+ds-6_amd64.deb Checksums-Sha256: 7f6c30cdb85fa320694fd8f72065546d45a487df030814893963d3fc246483ac 7748 iva_1.0.9+ds-6_amd64.buildinfo 8257ea3a3b6e0c8b6db11b40cf56a794d98af3342ec452ca80a37c0a43111909 8578168 iva_1.0.9+ds-6_amd64.deb Files: 962047fc597c19f3d18858982101356d 7748 science optional iva_1.0.9+ds-6_amd64.buildinfo fb458f5cea72cd1743dcd6706d5870a7 8578168 science optional iva_1.0.9+ds-6_amd64.deb Sat Dec 4 16:29:06 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/iva_1.0.9+ds-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/iva_1.0.9+ds-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/iva_1.0.9+ds-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/b1/iva_1.0.9+ds-6_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.BMeH8k8oCC/b2/iva_1.0.9+ds-6_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.310s) 0.310s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.107s) 0.107s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat Dec 4 16:29:07 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Sat Dec 4 16:29:07 UTC 2021 I: iva from buster built successfully and reproducibly on amd64. Sat Dec 4 16:29:09 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Dec 4 16:29:09 UTC 2021 I: Submitting 12K b1/iva_1.0.9+ds-6_amd64.buildinfo.asc Sat Dec 4 16:29:10 UTC 2021 I: Submitting 12K b2/iva_1.0.9+ds-6_amd64.buildinfo.asc Sat Dec 4 16:29:12 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Dec 4 16:29:12 UTC 2021 I: Done submitting .buildinfo files. Sat Dec 4 16:29:12 UTC 2021 I: Removing signed iva_1.0.9+ds-6_amd64.buildinfo.asc files: removed './b1/iva_1.0.9+ds-6_amd64.buildinfo.asc' removed './b2/iva_1.0.9+ds-6_amd64.buildinfo.asc'