I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 1 01:47:26 -12 2023 I: pbuilder-time-stamp: 1672580846 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 [ariba_2.13.3+ds-1.dsc] I: copying [./ariba_2.13.3+ds.orig.tar.xz] I: copying [./ariba_2.13.3+ds-1.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 Fri Jan 4 22:59:12 2019 -12 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.13.3+ds-1.dsc dpkg-source: info: extracting ariba in ariba-2.13.3+ds dpkg-source: info: unpacking ariba_2.13.3+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.13.3+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/699438/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='334ed3ee55a04cd4832784485f7456fd' 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='699438' 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.AMsWyNV1rW/pbuilderrc_EKJS --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.AMsWyNV1rW/b1 --logfile b1/build.log ariba_2.13.3+ds-1.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos5-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 16:21 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/699438/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), python3-biopython, python3-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4, python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-4~), mummer, fastaq (>= 3.12.0), help2man, asciidoctor 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 python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer (>= 0.10.2); however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.9.1); however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-nose (>= 1.3); however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-bs4; however: Package python3-bs4 is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2 (>= 2.1.0); however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on libminimap-dev; however: Package libminimap-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev (>= 0.1-4~); however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 3.12.0); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bowtie2{a} bsdmainutils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-lyx{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcapnp-0.7.0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libgfortran5{a} libglib2.0-0{a} libgsl23{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts2{a} libicu63{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{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} libminimap-dev{a} libminimap0{a} libmpdec2{a} libmurmurhash1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libruby2.5{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtbb2{a} libtcl8.6{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libyaml-0-2{a} lsb-base{a} m4{a} man-db{a} mash{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} python{a} python-matplotlib-data{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-biopython{a} python3-bs4{a} python3-cycler{a} python3-dateutil{a} python3-dendropy{a} python3-dev{a} python3-distutils{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pymummer{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-six{a} python3-soupsieve{a} python3-tk{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} samtools{a} sensible-utils{a} tk8.6-blt2.5{a} ttf-bitstream-vera{a} ucf{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl cwltool fonts-lato javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-chardet python3-lxml python3-olefile python3-renderpm shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 172 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After unpacking 349 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 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 42 http://deb.debian.org/debian buster/main amd64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libruby2.5 amd64 2.5.5-3+deb10u3 [3438 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 ruby2.5 amd64 2.5.5-3+deb10u3 [400 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 ruby amd64 1:2.5.1 [11.3 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4 [587 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 blt amd64 2.5.3+dfsg-4 [14.8 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 cd-hit amd64 4.6.8-2 [521 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 fastaq all 3.17.0-2 [47.8 kB] Get: 121 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get: 122 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 123 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 124 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 125 http://deb.debian.org/debian buster/main amd64 libcapnp-0.7.0 amd64 0.7.0-3 [1025 kB] Get: 126 http://deb.debian.org/debian buster/main amd64 libexpat1-dev amd64 2.2.6-2+deb10u1 [153 kB] Get: 127 http://deb.debian.org/debian buster/main amd64 libfml0 amd64 0.1-5 [69.3 kB] Get: 128 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 129 http://deb.debian.org/debian buster/main amd64 libfml-dev amd64 0.1-5 [81.4 kB] Get: 130 http://deb.debian.org/debian buster/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get: 131 http://deb.debian.org/debian buster/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get: 132 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 133 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 134 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get: 135 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get: 136 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get: 137 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 138 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get: 139 http://deb.debian.org/debian buster/main amd64 libminimap0 amd64 0.2-4 [23.0 kB] Get: 140 http://deb.debian.org/debian buster/main amd64 libminimap-dev amd64 0.2-4 [33.8 kB] Get: 141 http://deb.debian.org/debian buster/main amd64 libmurmurhash1 amd64 1.3-2 [5556 B] Get: 142 http://deb.debian.org/debian buster/main amd64 libpython3.7 amd64 3.7.3-2+deb10u3 [1498 kB] Get: 143 http://deb.debian.org/debian buster/main amd64 libpython3.7-dev amd64 3.7.3-2+deb10u3 [48.4 MB] Get: 144 http://deb.debian.org/debian buster/main amd64 libpython3-dev amd64 3.7.3-1 [20.1 kB] Get: 145 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get: 146 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u2 [271 kB] Get: 147 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get: 148 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get: 149 http://deb.debian.org/debian buster/main amd64 mash amd64 2.1+dfsg-2 [149 kB] Get: 150 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get: 151 http://deb.debian.org/debian buster/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get: 152 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get: 153 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get: 154 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u2 [395 kB] Get: 155 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get: 156 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get: 157 http://deb.debian.org/debian buster/main amd64 python3-soupsieve all 1.8+dfsg-1 [27.6 kB] Get: 158 http://deb.debian.org/debian buster/main amd64 python3-bs4 all 4.7.1-1 [94.1 kB] Get: 159 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get: 160 http://deb.debian.org/debian buster/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get: 161 http://deb.debian.org/debian buster/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get: 162 http://deb.debian.org/debian buster/main amd64 python3-dendropy all 4.4.0-1 [265 kB] Get: 163 http://deb.debian.org/debian buster/main amd64 python3.7-dev amd64 3.7.3-2+deb10u3 [510 kB] Get: 164 http://deb.debian.org/debian buster/main amd64 python3-dev amd64 3.7.3-1 [1264 B] Get: 165 http://deb.debian.org/debian buster/main amd64 python3-kiwisolver amd64 1.0.1-2+b1 [65.4 kB] Get: 166 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 167 http://deb.debian.org/debian buster/main amd64 python3-matplotlib amd64 3.0.2-2 [5353 kB] Get: 168 http://deb.debian.org/debian buster/main amd64 python3-nose all 1.3.7-4 [132 kB] Get: 169 http://deb.debian.org/debian buster/main amd64 python3-pymummer all 0.10.3-2 [9268 B] Get: 170 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get: 171 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Get: 172 http://deb.debian.org/debian buster/main amd64 python3-tk amd64 3.7.3-1 [97.4 kB] Fetched 122 MB in 2s (79.6 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 .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_amd64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_amd64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u7_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... 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Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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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 ... 20714 files and directories currently installed.) Preparing to unpack .../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 .../liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... 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Setting up gawk (1:4.2.1+dfsg-1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.2-1) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. 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 libcapnp-0.7.0:amd64 (0.7.0-3) ... Setting up libfml0 (0.1-5) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... 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 libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up libminimap0 (0.2-4) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:amd64 (2.2.6-2+deb10u1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up mash (2.1+dfsg-2) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... 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 zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up mummer (3.23+dfsg-4) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up ruby-xmlrpc (0.3.0-2) ... 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 libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libfml-dev (0.1-5) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython3.7:amd64 (3.7.3-2+deb10u3) ... Setting up libtool (2.4.6-9) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libpython3.7-dev:amd64 (3.7.3-2+deb10u3) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up python2 (2.7.16-1) ... 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 libpython-stdlib:amd64 (2.7.16-1) ... 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 libjs-jquery-ui (1.12.1+dfsg-5) ... 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 libminimap-dev (0.2-4) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up python (2.7.16-1) ... 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 libpython3-dev:amd64 (3.7.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.7-dev (3.7.3-2+deb10u3) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u2) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-soupsieve (1.8+dfsg-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 libxft2:amd64 (2.3.2-2) ... 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 libtk8.6:amd64 (8.6.9-2) ... Setting up python3-nose (1.3.7-4) ... Setting up python3-bs4 (4.7.1-1) ... Setting up samtools (1.9-4) ... Setting up python3-dev (3.7.3-1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-biopython (1.73+dfsg-1) ... Setting up python3-dendropy (4.4.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up blt (2.5.3+dfsg-4) ... Setting up fastaq (3.17.0-2) ... Setting up python3-tk:amd64 (3.7.3-1) ... Setting up python3-pymummer (0.10.3-2) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up libruby2.5:amd64 (2.5.5-3+deb10u3) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ruby2.5 (2.5.5-3+deb10u3) ... Setting up debhelper (12.1.1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... 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. 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/ariba-2.13.3+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 > ../ariba_2.13.3+ds-1_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.13.3+ds-1 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/ariba-2.13.3+ds' rm -rf /build/ariba-2.13.3+ds/debian/man dh_auto_clean -- I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it make[1]: Leaving directory '/build/ariba-2.13.3+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 running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/cluster.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/summary_cluster.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/card_record.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/assembly.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/bam_parse.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/summary.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/flag.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/clusters.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/report_flag_expander.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/vfdb_parser.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/ref_genes_getter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/mlst_profile.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/cdhit.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/sequence_metadata.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/pubmlst_getter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/ref_preparer.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/mapping.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/report.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/__init__.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/megares_zip_parser.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/external_progs.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/read_store.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/read_filter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/histogram.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/tb.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/samtools_variants.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/megares_data_finder.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/reference_data.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/scaffold_graph.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/mlst_reporter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/common.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/aln_to_metadata.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/sequence_variant.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/report_filter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/refdata_query.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/assembly_variants.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/link.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/faidx.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/summary_sample.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/mic_plotter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/versions.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba copying ariba/assembly_compare.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba creating /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks creating /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data creating /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data running build_ext building 'minimap_ariba' extension creating build creating build/temp.linux-amd64-3.7 creating build/temp.linux-amd64-3.7/ariba creating build/temp.linux-amd64-3.7/ariba/ext x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.7m -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o ariba/ext/minimap_ariba.cpp: In function 'bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)': ariba/ext/minimap_ariba.cpp:371:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] startOk = (r->qs < endTolerance || r->rs < endTolerance); ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o -o /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/minimap_ariba.cpython-37m-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/fml-asm_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/fml-asm_ariba.o -o /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/fermilite_ariba.cpython-37m-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/vcfcall_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/ariba-2.13.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/vcfcall_ariba.o -o /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/vcfcall_ariba.cpython-37m-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.7 copying and adjusting scripts/ariba -> build/scripts-3.7 changing mode of build/scripts-3.7/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build; python3.7 -m nose -v ---------------------------------------------------------------------- Ran 0 tests in 1.174s OK 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/ariba-2.13.3+ds/debian/ariba running install running build running build_py running build_ext running build_scripts running install_lib creating /build/ariba-2.13.3+ds/debian/ariba/usr creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7 creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/vcfcall_ariba.cpython-37m-x86_64-linux-gnu.so -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/fermilite_ariba.cpython-37m-x86_64-linux-gnu.so -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/minimap_ariba.cpython-37m-x86_64-linux-gnu.so -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/summary.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/report_flag_expander.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/vfdb_parser.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/refdata_query.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/read_filter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/versions.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/mic_plotter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/megares_data_finder.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/faidx.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/ref_preparer.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/tb.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/sequence_metadata.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/reference_data.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/report_filter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/read_store.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/summary_cluster.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/summary_sample.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/mlst_profile.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/mlst_reporter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/histogram.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/clusters.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/samtools_variants.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/report.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/flag.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/cluster.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/cdhit.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/card_record.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/assembly_variants.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/assembly_compare.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/external_progs.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/link.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/scaffold_graph.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/bam_parse.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/mapping.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/common.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/assembly.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/sequence_variant.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__pycache__/__init__.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__pycache__ creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20181221.json -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20181115.json -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20190102.json -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb_data creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data/reads_1.fq -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data/reads_2.fq -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data/metadata.tsv -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/test_run_data creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks creating /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/version.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/test.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/summary.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/run.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/refquery.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/micplot.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/getref.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/flag.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__pycache__/__init__.cpython-37.pyc -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/pubmlstget.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/test.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/prepareref_tb.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/micplot.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/reportfilter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/refquery.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/prepareref.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/aln2meta.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/__init__.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/version.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/getref.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/flag.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/summary.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/run.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tasks/expandflag.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/assembly_compare.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/versions.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/mic_plotter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/summary_sample.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/faidx.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/link.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/assembly_variants.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/refdata_query.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/report_filter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/sequence_variant.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/aln_to_metadata.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/ref_seq_chooser.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/common.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/mlst_reporter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/scaffold_graph.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/reference_data.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/megares_data_finder.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/samtools_variants.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/tb.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/histogram.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/read_filter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/read_store.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/external_progs.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/megares_zip_parser.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/__init__.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/report.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/mapping.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/ref_preparer.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/pubmlst_getter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/sequence_metadata.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/cdhit.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/mlst_profile.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/ref_genes_getter.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/vfdb_parser.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/report_flag_expander.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/clusters.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/flag.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/summary.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/bam_parse.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/assembly.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/summary_cluster_variant.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/card_record.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/summary_cluster.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/cluster.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba copying /build/ariba-2.13.3+ds/.pybuild/cpython3_3.7_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/test.py to test.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/micplot.py to micplot.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/refquery.py to refquery.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/__init__.py to __init__.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/version.py to version.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/getref.py to getref.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/flag.py to flag.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/summary.py to summary.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/run.py to run.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/versions.py to versions.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/summary_sample.py to summary_sample.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/faidx.py to faidx.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/link.py to link.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/refdata_query.py to refdata_query.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/report_filter.py to report_filter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/common.py to common.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/reference_data.py to reference_data.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/tb.py to tb.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/histogram.py to histogram.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/read_filter.py to read_filter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/read_store.py to read_store.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/external_progs.py to external_progs.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/__init__.py to __init__.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/report.py to report.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/mapping.py to mapping.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/cdhit.py to cdhit.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/clusters.py to clusters.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/flag.py to flag.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/summary.py to summary.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/bam_parse.py to bam_parse.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/assembly.py to assembly.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/card_record.py to card_record.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/cluster.py to cluster.cpython-37.pyc byte-compiling /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-37.pyc running install_egg_info running egg_info creating ariba.egg-info writing ariba.egg-info/PKG-INFO writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing top-level names to ariba.egg-info/top_level.txt writing manifest file 'ariba.egg-info/SOURCES.txt' reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /build/ariba-2.13.3+ds/debian/ariba/usr/lib/python3.7/dist-packages/ariba-2.13.3.egg-info Skipping SOURCES.txt running install_scripts creating /build/ariba-2.13.3+ds/debian/ariba/usr/bin copying build/scripts-3.7/ariba -> /build/ariba-2.13.3+ds/debian/ariba/usr/bin changing mode of /build/ariba-2.13.3+ds/debian/ariba/usr/bin/ariba to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/ariba-2.13.3+ds' mkdir -p /build/ariba-2.13.3+ds/debian/man asciidoctor -a docdate='' -b manpage -o /build/ariba-2.13.3+ds/debian/man/ariba.1 /build/ariba-2.13.3+ds/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/build/ariba-2.13.3+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 dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/fermilite_ariba.cpython-37m-x86_64-linux-gnu.so debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-37m-x86_64-linux-gnu.so debian/ariba/usr/lib/python3/dist-packages/minimap_ariba.cpython-37m-x86_64-linux-gnu.so were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ariba-dbgsym' in '../ariba-dbgsym_2.13.3+ds-1_amd64.deb'. dpkg-deb: building package 'ariba' in '../ariba_2.13.3+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ariba_2.13.3+ds-1_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: including full 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/699438 and its subdirectories I: Current time: Sun Jan 1 01:48:45 -12 2023 I: pbuilder-time-stamp: 1672580925