I: pbuilder: network access will be disabled during build I: Current time: Fri May 13 14:47:26 +14 2022 I: pbuilder-time-stamp: 1652402846 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 [kineticstools_0.6.1+git20180425.27a1878-2.dsc] I: copying [./kineticstools_0.6.1+git20180425.27a1878.orig.tar.xz] I: copying [./kineticstools_0.6.1+git20180425.27a1878-2.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 Feb 15 02:44:42 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kineticstools_0.6.1+git20180425.27a1878-2.dsc dpkg-source: info: extracting kineticstools in kineticstools-0.6.1+git20180425.27a1878 dpkg-source: info: unpacking kineticstools_0.6.1+git20180425.27a1878.orig.tar.xz dpkg-source: info: unpacking kineticstools_0.6.1+git20180425.27a1878-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying man-pages.patch dpkg-source: info: applying tests-import.patch dpkg-source: info: applying verbose-testing.patch dpkg-source: info: applying deactivate-tests-requiring-unavailable-data.patch dpkg-source: info: applying compiled-extension.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying ignore_h5py_deprecation_warnings_in_test.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15587/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/15587/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/15587/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0161f7ca262c4c02b5cef24c388ffba0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=15587 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Vb8bTHwPRJ/pbuilderrc_IZ0y --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Vb8bTHwPRJ/b2 --logfile b2/build.log kineticstools_0.6.1+git20180425.27a1878-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-0.bpo.4-amd64 #1 SMP Debian 5.10.19-1~bpo10+1 (2021-03-13) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 May 13 14:47 sh -> bash lrwxrwxrwx 1 root root 4 May 11 04:46 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/15587/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, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy, python-h5py, python-scipy, python-pytest 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 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-docutils; however: Package python-docutils is not installed. pbuilder-satisfydepends-dummy depends on python-pbcore (>= 1.2.8); however: Package python-pbcore is not installed. pbuilder-satisfydepends-dummy depends on python-pbcommand (>= 0.3.22); however: Package python-pbcommand is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-h5py; however: Package python-h5py is not installed. pbuilder-satisfydepends-dummy depends on python-scipy; however: Package python-scipy is not installed. pbuilder-satisfydepends-dummy depends on python-pytest; however: Package python-pytest 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} docutils-common{a} dwz{a} file{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} 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} m4{a} man-db{a} mime-support{a} openssl{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-decorator{a} python-docutils{a} python-funcsigs{a} python-h5py{a} python-idna{a} python-iso8601{a} python-minimal{a} python-more-itertools{a} python-numpy{a} python-pathlib2{a} python-pbcommand{a} python-pbcore{a} python-pkg-resources{a} python-pluggy{a} python-py{a} python-pysam{a} python-pytest{a} python-requests{a} python-roman{a} python-scandir{a} python-scipy{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} sgml-base{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl docutils-doc krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python-cryptography python-dev python-ipaddress python-openssl python-pil python-pygments shared-mime-info wget xdg-user-dirs 0 packages upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 63.3 MB of archives. After unpacking 229 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+deb10u5 [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 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 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+deb10u5 [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+deb10u2 [1258 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+deb10u1 [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 xml-core all 0.18+nmu1 [23.8 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 docutils-common all 0.14+dfsg-4 [167 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u1 [330 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get: 84 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-11 [305 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 python-all amd64 2.7.16-1 [1044 B] Get: 88 http://deb.debian.org/debian buster/main amd64 python-atomicwrites all 1.1.5-2 [6808 B] Get: 89 http://deb.debian.org/debian buster/main amd64 python-attr all 18.2.0-1 [37.2 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 python-avro all 1.8.2+dfsg-2 [59.4 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 python-certifi all 2018.8.24-1 [140 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 python-chardet all 3.0.4-3 [80.6 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 python-decorator all 4.3.0-1.1 [14.4 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 python-roman all 2.0.0-3 [8688 B] Get: 96 http://deb.debian.org/debian buster/main amd64 python-docutils all 0.14+dfsg-4 [379 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 python-funcsigs all 1.0.2-4 [13.7 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-six all 1.12.0-1 [15.7 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python-h5py amd64 2.8.0-3 [693 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 python-idna all 2.6-1 [34.1 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 python-iso8601 all 0.1.11-1 [12.7 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 python-more-itertools all 4.2.0-1 [42.3 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 python-scandir amd64 1.9.0-2 [18.3 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 python-pathlib2 all 2.3.3-1 [18.3 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 python-tz all 2019.1-1 [33.6 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 python-pbcommand all 1.1.1-1 [88.7 kB] Get: 110 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get: 111 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get: 112 http://deb.debian.org/debian buster/main amd64 python-pluggy all 0.8.0-1 [20.5 kB] Get: 113 http://deb.debian.org/debian buster/main amd64 python-py all 1.7.0-2 [86.5 kB] Get: 114 http://deb.debian.org/debian buster/main amd64 python-pytest all 3.10.1-2 [243 kB] Get: 115 http://deb.debian.org/debian buster/main amd64 python-scipy amd64 1.1.0-7 [10.1 MB] Get: 116 http://deb.debian.org/debian buster/main amd64 python-setuptools all 40.8.0-1 [382 kB] Fetched 63.3 MB in 2s (41.1 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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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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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+deb10u5) ... 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 ... 20945 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 ... 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Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-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 .../04-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../07-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../08-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. 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Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../16-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../17-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 .../18-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 .../19-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 .../20-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../21-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../22-libglib2.0-0_2.58.3-2+deb10u2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../23-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.9.4+dfsg1-7+deb10u1_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../25-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../26-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. 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Preparing to unpack .../87-python-setuptools_40.8.0-1_all.deb ... Unpacking python-setuptools (40.8.0-1) ... Setting up libpipeline1:amd64 (1.5.1-2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up sgml-base (1.29) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up openssl (1.1.1d-0+deb10u5) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u1) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... 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+deb10u1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... 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 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 python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u1) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up libhts2:amd64 (1.9-11) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python-iso8601 (0.1.11-1) ... Setting up python-all (2.7.16-1) ... Setting up python-attr (18.2.0-1) ... Setting up python-certifi (2018.8.24-1) ... Setting up python-atomicwrites (1.1.5-2) ... Setting up python-decorator (4.3.0-1.1) ... Setting up python-six (1.12.0-1) ... Setting up python-more-itertools (4.2.0-1) ... Setting up python-pluggy (0.8.0-1) ... Setting up python-idna (2.6-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-avro (1.8.2+dfsg-2) ... Setting up python-roman (2.0.0-3) ... Setting up python-funcsigs (1.0.2-4) ... Setting up python-tz (2019.1-1) ... Setting up python-scandir (1.9.0-2) ... Setting up python-chardet (3.0.4-3) ... Setting up python-py (1.7.0-2) ... Setting up python-urllib3 (1.24.1-1) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-pathlib2 (2.3.3-1) ... Setting up python-pytest (3.10.1-2) ... Setting up python-requests (2.21.0-1) ... Setting up python-scipy (1.1.0-7) ... Setting up python-h5py (2.8.0-3) ... Setting up python-pbcore (1.6.5+dfsg-1) ... Setting up python-pbcommand (1.1.1-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode 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/kineticstools-0.6.1+git20180425.27a1878/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package kineticstools dpkg-buildpackage: info: source version 0.6.1+git20180425.27a1878-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean running clean removing '/build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/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 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 dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/ipdModel.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/summarizeModifications.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/sharedArray.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/pipelineTools.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/ipdSummary.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/WorkerProcess.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/ResultWriter.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/ReferenceUtils.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/PositiveControlEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/MultiSiteDetection.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/MultiSiteCommon.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/ModificationDecode.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/MixtureEstimationMethods.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/MedakaLdaEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/KineticWorker.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools copying kineticsTools/BasicLdaEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools creating /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks copying kineticsTools/tasks/gather_kinetics_h5.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks copying kineticsTools/tasks/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks creating /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal copying kineticsTools/internal/basic.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal copying kineticsTools/internal/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal creating /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/unknown.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/XL-XL.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/XL-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/SP2-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/P6-C4.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/P5-C3.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/P4-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources copying kineticsTools/resources/C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources running build_ext building 'kineticsTools/tree_predict' extension creating build creating build/temp.linux-amd64-2.7 creating build/temp.linux-amd64-2.7/kineticsTools x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/kineticstools-0.6.1+git20180425.27a1878=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c kineticsTools/tree_predict.c -o build/temp.linux-amd64-2.7/kineticsTools/tree_predict.o -O3 -shared -std=c99 x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/kineticstools-0.6.1+git20180425.27a1878=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-2.7/kineticsTools/tree_predict.o -o /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tree_predict.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build; python2.7 -m pytest test ============================= test session starts ============================== platform linux2 -- Python 2.7.16, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 rootdir: /build/kineticstools-0.6.1+git20180425.27a1878, inifile: collected 29 items test/test_ReferenceUtils.py ssssss [ 20%] test/test_gather_h5.py ... [ 31%] test/test_inputs.py ssssssssss [ 65%] test/test_internal.py .... [ 79%] test/test_outputs.py sss [ 89%] test/test_tool_contract.py sss [100%] =============================== 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 =============== 7 passed, 22 skipped, 4 warnings in 4.42 seconds =============== 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 debian/rules override_dh_auto_install make[1]: Entering directory '/build/kineticstools-0.6.1+git20180425.27a1878' dh_auto_install I: pybuild base:217: /usr/bin/python setup.py install --root /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools running install running build running build_py running build_ext running install_lib creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7 creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/sharedArray.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdModel.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/WorkerProcess.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ModificationDecode.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/PositiveControlEnricher.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/BasicLdaEnricher.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MedakaLdaEnricher.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteDetection.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteCommon.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MixtureEstimationMethods.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/KineticWorker.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/pipelineTools.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ResultWriter.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ReferenceUtils.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/__init__.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tree_predict.so -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P4-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P5-C3.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P6-C4.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/SP2-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/XL-C2.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/XL-XL.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/unknown.h5 -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/basic.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/__init__.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/basic.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal creating /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/gather_kinetics_h5.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/__init__.pyc -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/gather_kinetics_h5.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/BasicLdaEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/KineticWorker.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MedakaLdaEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MixtureEstimationMethods.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ModificationDecode.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteCommon.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteDetection.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/PositiveControlEnricher.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ReferenceUtils.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ResultWriter.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/WorkerProcess.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/__init__.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdSummary.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/pipelineTools.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/sharedArray.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/summarizeModifications.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools copying /build/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdModel.py -> /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal/__init__.py to __init__.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal/basic.py to basic.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py to __init__.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py to gather_kinetics_h5.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/__init__.py to __init__.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py to sharedArray.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.pyc byte-compiling /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py to ipdModel.pyc running install_egg_info running egg_info creating kineticsTools.egg-info writing requirements to kineticsTools.egg-info/requires.txt writing kineticsTools.egg-info/PKG-INFO writing top-level names to kineticsTools.egg-info/top_level.txt writing dependency_links to kineticsTools.egg-info/dependency_links.txt writing entry points to kineticsTools.egg-info/entry_points.txt writing manifest file 'kineticsTools.egg-info/SOURCES.txt' reading manifest file 'kineticsTools.egg-info/SOURCES.txt' writing manifest file 'kineticsTools.egg-info/SOURCES.txt' Copying kineticsTools.egg-info to /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info Skipping SOURCES.txt running install_scripts Installing ipdSummary script to /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/bin Installing summarizeModifications script to /build/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/bin mkdir -p /build/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/bin mv debian/python-kineticstools/usr/bin/* /build/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/bin mkdir -p /build/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/share/man//man1 rst2man doc/manual.rst > /build/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/share/man//man1/ipdSummary.1 doc/manual.rst:117: (ERROR/3) Malformed table. Text in column margin in table line 2. ================ =========== Column Description ================ =========== seqid Fasta contig name source Name of tool -- 'kinModCall' type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature start Modification position on contig end Modification position on contig score Phred transformed p-value of detection - this is the single-site detection p-value strand Sample strand containing modification phase Not applicable attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes. ================ =========== doc/manual.rst:46: (WARNING/2) "math" role not supported doc/manual.rst:48: (WARNING/2) "math" role not supported doc/manual.rst:48: (WARNING/2) "math" role not supported mkdir -p debian/kineticstools-data/usr/share/kineticstools mv debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/ make[1]: Leaving directory '/build/kineticstools-0.6.1+git20180425.27a1878' 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/kineticstools/usr/bin/summarizeModifications I: dh_python2 tools:114: replacing shebang in debian/kineticstools/usr/bin/ipdSummary I: dh_python2 fs:343: renaming tree_predict.so to tree_predict.x86_64-linux-gnu.so 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_dwz -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/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python-kineticstools' in '../python-kineticstools_0.6.1+git20180425.27a1878-2_amd64.deb'. dpkg-deb: building package 'kineticstools-data' in '../kineticstools-data_0.6.1+git20180425.27a1878-2_all.deb'. dpkg-deb: building package 'python-kineticstools-dbgsym' in '../python-kineticstools-dbgsym_0.6.1+git20180425.27a1878-2_amd64.deb'. dpkg-deb: building package 'kineticstools' in '../kineticstools_0.6.1+git20180425.27a1878-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../kineticstools_0.6.1+git20180425.27a1878-2_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: user script /srv/workspace/pbuilder/15587/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/15587/tmp/hooks/B01_cleanup finished 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/15587 and its subdirectories I: Current time: Fri May 13 14:50:47 +14 2022 I: pbuilder-time-stamp: 1652403047