I: pbuilder: network access will be disabled during build I: Current time: Sat Sep 10 08:43:35 -12 2022 I: pbuilder-time-stamp: 1662842615 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 [pbgenomicconsensus_2.3.2-5.dsc] I: copying [./pbgenomicconsensus_2.3.2.orig.tar.gz] I: copying [./pbgenomicconsensus_2.3.2-5.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 Sun Apr 7 03:16:55 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbgenomicconsensus_2.3.2-5.dsc dpkg-source: info: extracting pbgenomicconsensus in pbgenomicconsensus-2.3.2 dpkg-source: info: unpacking pbgenomicconsensus_2.3.2.orig.tar.gz dpkg-source: info: unpacking pbgenomicconsensus_2.3.2-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying verbose-testing.patch dpkg-source: info: applying disable-arrow-tests.patch dpkg-source: info: applying no-poa-convenience-script.patch dpkg-source: info: applying ignore_test_requiring_pbtestdata.patch dpkg-source: info: applying ignore_test_using_local_data.patch dpkg-source: info: applying ignore_warnings.patch dpkg-source: info: applying use_frombuffer.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31840/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='c61fd38c88e64c989e008e8e1889cff6' 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='31840' 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.NGsAPdt8TS/pbuilderrc_Nb4p --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.NGsAPdt8TS/b1 --logfile b1/build.log pbgenomicconsensus_2.3.2-5.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 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) 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 Sep 9 02:46 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/31840/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 (>= 12~), dh-python, pandoc, python-pkg-resources, python-all, python-setuptools, python-pbconsensuscore, python-pbcore (>= 1.2.9), python-pbcommand (>= 0.3.20), python-h5py, python-numpy, python-nose, python-cram, python-pytest, python-consensuscore2, mummer, exonerate 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 (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python-pkg-resources; however: Package python-pkg-resources is not installed. pbuilder-satisfydepends-dummy depends on python-all; however: Package python-all is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python-pbconsensuscore; however: Package python-pbconsensuscore is not installed. pbuilder-satisfydepends-dummy depends on python-pbcore (>= 1.2.9); however: Package python-pbcore is not installed. pbuilder-satisfydepends-dummy depends on python-pbcommand (>= 0.3.20); however: Package python-pbcommand is not installed. pbuilder-satisfydepends-dummy depends on python-h5py; however: Package python-h5py is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-nose; however: Package python-nose is not installed. pbuilder-satisfydepends-dummy depends on python-cram; however: Package python-cram is not installed. pbuilder-satisfydepends-dummy depends on python-pytest; however: Package python-pytest is not installed. pbuilder-satisfydepends-dummy depends on python-consensuscore2; however: Package python-consensuscore2 is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} exonerate{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhdf5-103{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} liblua5.1-0{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mime-support{a} mummer{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} python{a} python-all{a} python-atomicwrites{a} python-attr{a} python-avro{a} python-certifi{a} python-chardet{a} python-consensuscore2{a} python-cram{a} python-funcsigs{a} python-h5py{a} python-idna{a} python-iso8601{a} python-minimal{a} python-more-itertools{a} python-nose{a} python-numpy{a} python-pathlib2{a} python-pbcommand{a} python-pbconsensuscore{a} python-pbcore{a} python-pkg-resources{a} python-pluggy{a} python-py{a} python-pysam{a} python-pytest{a} python-requests{a} python-scandir{a} python-setuptools{a} python-six{a} python-tz{a} python-urllib3{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python-cryptography python-ipaddress python-openssl shared-mime-info wget xdg-user-dirs 0 packages upgraded, 120 newly installed, 0 to remove and 0 not upgraded. Need to get 72.3 MB of archives. After unpacking 320 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+deb10u6 [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 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u6 [844 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 exonerate amd64 2.4.0-4 [1544 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get: 83 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 liblua5.1-0 amd64 5.1.5-8.1+b2 [111 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 pandoc-data all 2.2.1-3 [329 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 pandoc amd64 2.2.1-3+b2 [14.7 MB] Get: 91 http://deb.debian.org/debian buster/main amd64 python-all amd64 2.7.16-1 [1044 B] Get: 92 http://deb.debian.org/debian buster/main amd64 python-atomicwrites all 1.1.5-2 [6808 B] Get: 93 http://deb.debian.org/debian buster/main amd64 python-attr all 18.2.0-1 [37.2 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 python-avro all 1.8.2+dfsg-2 [59.4 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 python-certifi all 2018.8.24-1 [140 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 python-chardet all 3.0.4-3 [80.6 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 python-consensuscore2 amd64 3.3.0+dfsg-2.1 [611 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python-cram all 0.7-3 [17.0 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 python-funcsigs all 1.0.2-4 [13.7 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 python-six all 1.12.0-1 [15.7 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 python-h5py amd64 2.8.0-3 [693 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 python-idna all 2.6-1 [34.1 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 python-iso8601 all 0.1.11-1 [12.7 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 python-more-itertools all 4.2.0-1 [42.3 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 python-nose all 1.3.7-4 [132 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 python-scandir amd64 1.9.0-2 [18.3 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 python-pathlib2 all 2.3.3-1 [18.3 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 python-pbcommand all 1.1.1-1 [88.7 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 python-pbconsensuscore amd64 1.1.1+dfsg-1 [672 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get: 116 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get: 117 http://deb.debian.org/debian buster/main amd64 python-pluggy all 0.8.0-1 [20.5 kB] Get: 118 http://deb.debian.org/debian buster/main amd64 python-py all 1.7.0-2 [86.5 kB] Get: 119 http://deb.debian.org/debian buster/main amd64 python-pytest all 3.10.1-2 [243 kB] Get: 120 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] Fetched 72.3 MB in 2s (37.9 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+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u6) ... 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) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... 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 libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21123 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_amd64.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:amd64. Preparing to unpack .../libmpdec2_2.4.2-2_amd64.deb ... Unpacking libmpdec2:amd64 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:amd64. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u3_amd64.deb ... Unpacking python3.7 (3.7.3-2+deb10u3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.7.3-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21535 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_amd64.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package m4. Preparing to unpack .../06-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../07-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../08-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../09-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../10-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package openssl. Preparing to unpack .../11-openssl_1.1.1d-0+deb10u6_amd64.deb ... Unpacking openssl (1.1.1d-0+deb10u6) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../12-ca-certificates_20200601~deb10u2_all.deb ... Unpacking ca-certificates (20200601~deb10u2) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../17-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../18-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../19-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../20-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../21-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../22-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../23-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../24-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ... 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I: Building the package I: Running cd /build/pbgenomicconsensus-2.3.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package pbgenomicconsensus dpkg-buildpackage: info: source version 2.3.2-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Liubov Chuprikova dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbgenomicconsensus-2.3.2' rm -f /build/pbgenomicconsensus-2.3.2/debian/man/pbgff.5 /build/pbgenomicconsensus-2.3.2/debian/man/variantCaller.1 dh_auto_clean I: pybuild base:217: python2.7 setup.py clean running clean removing '/build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it make[1]: Leaving directory '/build/pbgenomicconsensus-2.3.2' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python2 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/pbgenomicconsensus-2.3.2' pandoc -s --to man /build/pbgenomicconsensus-2.3.2/debian/man/pbgff.5.md -o /build/pbgenomicconsensus-2.3.2/debian/man/pbgff.5 pandoc -s --to man /build/pbgenomicconsensus-2.3.2/debian/man/variantCaller.1.md -o /build/pbgenomicconsensus-2.3.2/debian/man/variantCaller.1 dh_auto_build I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/utils.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/windows.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/variants.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/reference.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/options.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/main.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/consensus.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/algorithmSelection.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/Worker.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus copying GenomicConsensus/ResultCollector.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver copying GenomicConsensus/quiver/model.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver copying GenomicConsensus/quiver/utils.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver copying GenomicConsensus/quiver/quiver.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver copying GenomicConsensus/quiver/diploid.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver copying GenomicConsensus/quiver/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/poa copying GenomicConsensus/poa/poa.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/poa copying GenomicConsensus/poa/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/poa creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/plurality copying GenomicConsensus/plurality/plurality.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/plurality copying GenomicConsensus/plurality/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/plurality creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io copying GenomicConsensus/io/utils.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io copying GenomicConsensus/io/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io copying GenomicConsensus/io/VariantsVcfWriter.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io copying GenomicConsensus/io/VariantsGffWriter.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow copying GenomicConsensus/arrow/utils.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow copying GenomicConsensus/arrow/model.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow copying GenomicConsensus/arrow/diploid.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow copying GenomicConsensus/arrow/arrow.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow copying GenomicConsensus/arrow/__init__.py -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow running egg_info creating GenomicConsensus.egg-info writing requirements to GenomicConsensus.egg-info/requires.txt writing GenomicConsensus.egg-info/PKG-INFO writing top-level names to GenomicConsensus.egg-info/top_level.txt writing dependency_links to GenomicConsensus.egg-info/dependency_links.txt writing manifest file 'GenomicConsensus.egg-info/SOURCES.txt' reading manifest file 'GenomicConsensus.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'GenomicConsensus.egg-info/SOURCES.txt' creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-03 creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-03/GenomicConsensus copying GenomicConsensus/quiver/resources/2013-03/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-03/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-05 creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-05/GenomicConsensus copying GenomicConsensus/quiver/resources/2013-05/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-05/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-09 creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-09/GenomicConsensus copying GenomicConsensus/quiver/resources/2013-09/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-09/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-03 creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-03/GenomicConsensus copying GenomicConsensus/quiver/resources/2014-03/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-03/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-09 creating /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus copying GenomicConsensus/quiver/resources/2014-09/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus running build_scripts creating build creating build/scripts-2.7 copying and adjusting bin/variantCaller -> build/scripts-2.7 copying and adjusting bin/summarizeConsensus -> build/scripts-2.7 copying and adjusting bin/gffToVcf -> build/scripts-2.7 copying and adjusting bin/gffToBed -> build/scripts-2.7 copying bin/plurality -> build/scripts-2.7 copying bin/poa -> build/scripts-2.7 copying bin/quiver -> build/scripts-2.7 copying bin/arrow -> build/scripts-2.7 changing mode of build/scripts-2.7/variantCaller from 644 to 755 changing mode of build/scripts-2.7/summarizeConsensus from 644 to 755 changing mode of build/scripts-2.7/gffToVcf from 644 to 755 changing mode of build/scripts-2.7/gffToBed from 644 to 755 make[1]: Leaving directory '/build/pbgenomicconsensus-2.3.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbgenomicconsensus-2.3.2' chmod +x bin/gffToBed unset GZIP ; \ PYTHONPATH=/build/pbgenomicconsensus-2.3.2 PATH=/build/pbgenomicconsensus-2.3.2/bin:$PATH /usr/bin/make -j1 tests make[2]: Entering directory '/build/pbgenomicconsensus-2.3.2' # Unit tests # ignore tests requiring https://github.com/PacificBiosciences/PacBioTestData which is not packaged set -e ; \ TMPDIR=$(mktemp -d /tmp/test_ignore_XXXXXX) ; \ mv tests/unit/test_tool_contract.py ${TMPDIR} ; \ py.test --junit-xml=nosetests.xml tests/unit ; \ rm -rf tests/unit/__pycache__ ; \ mv ${TMPDIR}/* tests/unit ; \ rmdir ${TMPDIR} ============================= test session starts ============================== platform linux2 -- Python 2.7.16, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 rootdir: /build/pbgenomicconsensus-2.3.2, inifile: collected 40 items tests/unit/test_algorithm_selection.py . [ 2%] tests/unit/test_consensus.py .. [ 7%] tests/unit/test_coverage_intervals.py ............ [ 37%] tests/unit/test_dinucleotide_repeats.py . [ 40%] tests/unit/test_diploid.py . [ 42%] tests/unit/test_plurality.py ... [ 50%] tests/unit/test_quiver.py ............. [ 82%] tests/unit/test_quiver_params.py ...... [ 97%] tests/unit/test_summarize_consensus.py . [100%] ------ generated xml file: /build/pbgenomicconsensus-2.3.2/nosetests.xml ------- =============================== warnings summary =============================== /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:75 /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:75: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead "ZZZZZZZ", dtype=np.uint8).reshape(7, 7) /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:83 /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:83: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead "ZZZZZZZ", dtype=np.uint8).reshape(7, 7) /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:91 /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:91: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead "ZZZZZZZ", dtype=np.uint8).reshape(7, 7) /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:99 /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:99: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead "ZZZZZZZ", dtype=np.uint8).reshape(7, 7) -- Docs: https://docs.pytest.org/en/latest/warnings.html ==================== 40 passed, 4 warnings in 1.00 seconds ===================== # End-to-end tests # some tests require a input files on a local mount of upstream # The test poa-all4mer.t contains a wrong syntax in calling poa - no idea how to fix this thus ignoring the test set -e ; \ TMPDIR=$(mktemp -d /tmp/test_ignore_XXXXXX) ; \ for nt in $(grep -Rl /mnt/secondary/Share/Quiver/ tests/*) ; do \ mkdir -p ${TMPDIR}/$(dirname ${nt}) ; \ mv ${nt} ${TMPDIR}/$(dirname ${nt}) ; \ done ; \ mkdir -p ${TMPDIR}/tests/cram ; \ mv tests/cram/poa-all4mer.t ${TMPDIR}/tests/cram ; \ PATH=`pwd`:/build/pbgenomicconsensus-2.3.2/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games cram --verbose --xunit-file=gc-cram.xml `ls tests/cram/*.t | grep -v -e arrow -e bad_input` ; \ cp -a -v ${TMPDIR}/tests/* tests ; \ rm -r ${TMPDIR} tests/cram/best-all4mer.t: passed tests/cram/convert-to-bed.t: passed tests/cram/convert-to-vcf.t: passed tests/cram/coverage-bed.t: passed tests/cram/plurality-all4mer.t: passed tests/cram/plurality-compressed.t: passed tests/cram/quiver-all4mer.t: passed tests/cram/quiver-empty.t: passed tests/cram/quiver-noqvs-test.t: passed tests/cram/reference-mismatch.t: passed tests/cram/version.t: passed tests/cram/zero-pws.t: passed # Ran 12 tests, 0 skipped, 0 failed. '/tmp/test_ignore_EFGqWK/tests/cram/alignment_summary.t' -> 'tests/cram/alignment_summary.t' '/tmp/test_ignore_EFGqWK/tests/cram/quiver-tinyLambda-coverage-islands.t' -> 'tests/cram/quiver-tinyLambda-coverage-islands.t' '/tmp/test_ignore_EFGqWK/tests/cram/poa-all4mer.t' -> 'tests/cram/poa-all4mer.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/arrow-sequel-6kEcoli.t' -> 'tests/cram/internal/arrow-sequel-6kEcoli.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/arrow-staph.t' -> 'tests/cram/internal/arrow-staph.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/plurality-diploid-lambda.t' -> 'tests/cram/internal/plurality-diploid-lambda.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/plurality-lambda.t' -> 'tests/cram/internal/plurality-lambda.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-compatibility.t' -> 'tests/cram/internal/quiver-compatibility.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-diploid-lambda.t' -> 'tests/cram/internal/quiver-diploid-lambda.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-ecoli.t' -> 'tests/cram/internal/quiver-ecoli.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-eichler-bac.t' -> 'tests/cram/internal/quiver-eichler-bac.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-fluidigm-amplicons.t' -> 'tests/cram/internal/quiver-fluidigm-amplicons.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-lambda.t' -> 'tests/cram/internal/quiver-lambda.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-mruber.t' -> 'tests/cram/internal/quiver-mruber.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-staph.t' -> 'tests/cram/internal/quiver-staph.t' '/tmp/test_ignore_EFGqWK/tests/cram/internal/quiver-stumpy-read.t.off' -> 'tests/cram/internal/quiver-stumpy-read.t.off' make[2]: Leaving directory '/build/pbgenomicconsensus-2.3.2' chmod -x bin/gffToBed make[1]: Leaving directory '/build/pbgenomicconsensus-2.3.2' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus running install running build running build_py running egg_info writing requirements to GenomicConsensus.egg-info/requires.txt writing GenomicConsensus.egg-info/PKG-INFO writing top-level names to GenomicConsensus.egg-info/top_level.txt writing dependency_links to GenomicConsensus.egg-info/dependency_links.txt reading manifest file 'GenomicConsensus.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'GenomicConsensus.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow/arrow.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow/diploid.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow/model.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/arrow/utils.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io/VariantsGffWriter.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io/VariantsVcfWriter.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/io/utils.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/plurality copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/plurality/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/plurality copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/plurality/plurality.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/plurality creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/poa copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/poa/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/poa copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/poa/poa.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/poa creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-09 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-09/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-03 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-03/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2014-03/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2014-03/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-09 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-09/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-09/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-09/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-05 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-05/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-05/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-05/GenomicConsensus creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-03 creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-03/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/resources/2013-03/GenomicConsensus/QuiverParameters.ini -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/resources/2013-03/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/diploid.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/quiver.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/utils.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/quiver/model.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/ResultCollector.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/Worker.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/__init__.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/algorithmSelection.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/consensus.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/main.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/options.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/reference.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/variants.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/windows.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus copying /build/pbgenomicconsensus-2.3.2/.pybuild/cpython2_2.7_pbgenomicconsensus/build/GenomicConsensus/utils.py -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow/arrow.py to arrow.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow/diploid.py to diploid.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow/model.py to model.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/arrow/utils.py to utils.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io/VariantsGffWriter.py to VariantsGffWriter.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io/VariantsVcfWriter.py to VariantsVcfWriter.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/io/utils.py to utils.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/plurality/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/plurality/plurality.py to plurality.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/poa/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/poa/poa.py to poa.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/diploid.py to diploid.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/quiver.py to quiver.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/utils.py to utils.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/quiver/model.py to model.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/ResultCollector.py to ResultCollector.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/Worker.py to Worker.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/__init__.py to __init__.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/algorithmSelection.py to algorithmSelection.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/consensus.py to consensus.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py to main.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/options.py to options.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py to reference.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/variants.py to variants.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py to windows.pyc byte-compiling /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus/utils.py to utils.pyc running install_egg_info Copying GenomicConsensus.egg-info to /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/lib/python2.7/dist-packages/GenomicConsensus-2.3.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/arrow -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/quiver -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/poa -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/plurality -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/gffToBed -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/gffToVcf -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/summarizeConsensus -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin copying build/scripts-2.7/variantCaller -> /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/arrow to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/quiver to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/poa to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/plurality to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/gffToBed to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/gffToVcf to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/summarizeConsensus to 755 changing mode of /build/pbgenomicconsensus-2.3.2/debian/python-pbgenomicconsensus/usr/bin/variantCaller to 755 debian/rules override_dh_install make[1]: Entering directory '/build/pbgenomicconsensus-2.3.2' dh_install mkdir -p /build/pbgenomicconsensus-2.3.2/debian/pbgenomicconsensus/usr/bin/ mv debian/python-pbgenomicconsensus/usr/bin/* /build/pbgenomicconsensus-2.3.2/debian/pbgenomicconsensus/usr/bin/ rm -f /build/pbgenomicconsensus-2.3.2/debian/pbgenomicconsensus/usr/bin//poa make[1]: Leaving directory '/build/pbgenomicconsensus-2.3.2' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 tools:114: replacing shebang in debian/pbgenomicconsensus/usr/bin/variantCaller I: dh_python2 tools:114: replacing shebang in debian/pbgenomicconsensus/usr/bin/summarizeConsensus I: dh_python2 tools:114: replacing shebang in debian/pbgenomicconsensus/usr/bin/gffToVcf I: dh_python2 tools:114: replacing shebang in debian/pbgenomicconsensus/usr/bin/gffToBed dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-pbgenomicconsensus: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-pbgenomicconsensus: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pbgenomicconsensus' in '../pbgenomicconsensus_2.3.2-5_all.deb'. dpkg-deb: building package 'python-pbgenomicconsensus' in '../python-pbgenomicconsensus_2.3.2-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbgenomicconsensus_2.3.2-5_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) 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/31840 and its subdirectories I: Current time: Sat Sep 10 08:45:00 -12 2022 I: pbuilder-time-stamp: 1662842700