Thu May 4 15:30:38 UTC 2023 I: starting to build kineticstools/bookworm/i386 on jenkins on '2023-05-04 15:30'
Thu May 4 15:30:38 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_7/8694/console.log
Thu May 4 15:30:38 UTC 2023 I: Downloading source for bookworm/kineticstools=0.6.1+git20220223.1326a4d+dfsg-2
--2023-05-04 15:30:39-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kineticstools/kineticstools_0.6.1%2bgit20220223.1326a4d%2bdfsg-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2101 (2.1K) [text/prs.lines.tag]
Saving to: ‘kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc’
0K .. 100% 9.36M=0s
2023-05-04 15:30:39 (9.36 MB/s) - ‘kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc’ saved [2101/2101]
Thu May 4 15:30:39 UTC 2023 I: kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: kineticstools
Binary: kineticstools, kineticstools-data, python3-kineticstools
Architecture: any all
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/PacificBiosciences/kineticsTools
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/kineticstools
Vcs-Git: https://salsa.debian.org/med-team/kineticstools.git
Testsuite: autopkgtest
Testsuite-Triggers: hdf5-tools, make, python3-cram, python3-pytest
Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-docutils, python3-pbcore, python3-pbcommand, python3-numpy, python3-h5py, python3-scipy, python3-uritools <!nocheck>, python3-pytest <!nocheck>, python3-pytest-runner <!nocheck>, python3-pytest-xdist <!nocheck>
Package-List:
kineticstools deb science optional arch=all
kineticstools-data deb science optional arch=all
python3-kineticstools deb python optional arch=any
Checksums-Sha1:
85654046ecd0a08535d85ddc2513a27e338d3aa5 21772620 kineticstools_0.6.1+git20220223.1326a4d+dfsg.orig.tar.xz
fe923326238a6592cee13ed73b9a90a69f5f0e46 10356 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.debian.tar.xz
Checksums-Sha256:
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529b2991756a712db0e2ecff9a3d10f78ed6ed47a178958a9ff27b8d0d514978 10356 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.debian.tar.xz
Files:
ce6810e2c6dd2abe5b525abab95370ea 21772620 kineticstools_0.6.1+git20220223.1326a4d+dfsg.orig.tar.xz
f4c2610d56e333da8d2f925c86db5871 10356 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.debian.tar.xz
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Thu May 4 15:30:39 UTC 2023 I: Checking whether the package is not for us
Thu May 4 15:30:39 UTC 2023 I: Starting 1st build on remote node ionos12-i386.debian.net.
Thu May 4 15:30:39 UTC 2023 I: Preparing to do remote build '1' on ionos12-i386.debian.net.
Thu May 4 15:34:08 UTC 2023 I: Deleting $TMPDIR on ionos12-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu May 4 03:30:41 -12 2023
I: pbuilder-time-stamp: 1683214241
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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: using eatmydata during job
I: Copying source file
I: copying [kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc]
I: copying [./kineticstools_0.6.1+git20220223.1326a4d+dfsg.orig.tar.xz]
I: copying [./kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Dec 21 02:37:16 2022 -12
gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc: no acceptable signature found
dpkg-source: info: extracting kineticstools in kineticstools-0.6.1+git20220223.1326a4d+dfsg
dpkg-source: info: unpacking kineticstools_0.6.1+git20220223.1326a4d+dfsg.orig.tar.xz
dpkg-source: info: unpacking kineticstools_0.6.1+git20220223.1326a4d+dfsg-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 spelling.patch
dpkg-source: info: applying tests2to3.patch
dpkg-source: info: applying man-align-cols.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/30953/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='1b2f1c2ca3ac419f8224f89a81d52099'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='30953'
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/r-b-build.SnodrAFS/pbuilderrc_O8p9 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/b1 --logfile b1/build.log kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos12-i386 5.10.0-22-686-pae #1 SMP Debian 5.10.178-3 (2023-04-22) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 23:43 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 22:20 more
-rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount
-rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 22:20 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/30953/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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-compat (= 13), dh-python, python3, python3-setuptools, python3-docutils, python3-pbcore, python3-pbcommand, python3-numpy, python3-h5py, python3-scipy, python3-uritools, python3-pytest, python3-pytest-runner, python3-pytest-xdist
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-docutils; however:
Package python3-docutils is not installed.
pbuilder-satisfydepends-dummy depends on python3-pbcore; however:
Package python3-pbcore is not installed.
pbuilder-satisfydepends-dummy depends on python3-pbcommand; however:
Package python3-pbcommand is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-h5py; however:
Package python3-h5py is not installed.
pbuilder-satisfydepends-dummy depends on python3-scipy; however:
Package python3-scipy is not installed.
pbuilder-satisfydepends-dummy depends on python3-uritools; however:
Package python3-uritools is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest-runner; however:
Package python3-pytest-runner is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however:
Package python3-pytest-xdist 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} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-hl-100{a} libhts3{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxsimd-dev{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} openssl{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-avro{a} python3-beniget{a} python3-biopython{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-execnet{a} python3-gast{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-iniconfig{a} python3-iso8601{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pbcommand{a} python3-pbcore{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-py{a} python3-pysam{a} python3-pytest{a} python3-pytest-runner{a} python3-pytest-xdist{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3-uritools{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl javascript-common libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-olefile python3-pygments shared-mime-info wget xdg-user-dirs
0 packages upgraded, 162 newly installed, 0 to remove and 0 not upgraded.
Need to get 112 MB of archives. After unpacking 539 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 mailcap all 3.70+nmu1 [32.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 mime-support all 3.66 [10.9 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 13 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.8-1 [1412 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-2 [131 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 fonts-urw-base35 all 20200910-7 [10.8 MB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libaec0 i386 1.0.6-1+b1 [22.4 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-20 [9510 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-9 [420 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 libsz2 i386 1.0.6-1+b1 [7884 B]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libhdf5-103-1 i386 1.10.8+repack1-1 [1175 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 libhdf5-hl-100 i386 1.10.8+repack1-1 [79.3 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 86 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 libopenblas0-pthread i386 0.3.21+ds-4 [5148 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 liblbfgsb0 i386 3.0+dfsg.4-1 [28.5 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB]
Get: 96 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 liblzf1 i386 3.6-3 [9668 B]
Get: 98 http://deb.debian.org/debian bookworm/main i386 libopenblas0 i386 0.3.21+ds-4 [32.6 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 libopenblas-pthread-dev i386 0.3.21+ds-4 [3447 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 libopenblas-dev i386 0.3.21+ds-4 [44.9 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-1+b1 [196 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B]
Get: 106 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B]
Get: 107 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB]
Get: 108 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.1 [293 kB]
Get: 109 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB]
Get: 110 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.1 [99.7 kB]
Get: 111 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.1 [111 kB]
Get: 112 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 113 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 114 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 115 http://deb.debian.org/debian bookworm/main i386 libxsimd-dev i386 8.1.0-7 [88.8 kB]
Get: 116 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B]
Get: 117 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB]
Get: 118 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB]
Get: 119 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B]
Get: 120 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB]
Get: 121 http://deb.debian.org/debian bookworm/main i386 python3-avro all 1.11.1+dfsg-2 [70.5 kB]
Get: 122 http://deb.debian.org/debian bookworm/main i386 python3-gast all 0.5.2-2 [9364 B]
Get: 123 http://deb.debian.org/debian bookworm/main i386 python3-beniget all 0.4.1-3 [9920 B]
Get: 124 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 125 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB]
Get: 126 http://deb.debian.org/debian bookworm/main i386 python3-renderpm i386 3.6.12-1+b1 [81.4 kB]
Get: 127 http://deb.debian.org/debian bookworm/main i386 python3-reportlab-accel i386 3.6.12-1+b1 [39.4 kB]
Get: 128 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB]
Get: 129 http://deb.debian.org/debian bookworm/main i386 python3-reportlab all 3.6.12-1 [564 kB]
Get: 130 http://deb.debian.org/debian bookworm/main i386 w3c-sgml-lib all 1.3-3 [273 kB]
Get: 131 http://deb.debian.org/debian bookworm/main i386 python3-biopython i386 1.80+dfsg-4+b1 [1589 kB]
Get: 132 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB]
Get: 133 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 134 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 135 http://deb.debian.org/debian bookworm/main i386 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 136 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B]
Get: 137 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 138 http://deb.debian.org/debian bookworm/main i386 python3-execnet all 1.9.0-1 [41.5 kB]
Get: 139 http://deb.debian.org/debian bookworm/main i386 python3-h5py-serial i386 3.7.0-8 [810 kB]
Get: 140 http://deb.debian.org/debian bookworm/main i386 python3-h5py all 3.7.0-8 [10.3 kB]
Get: 141 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB]
Get: 142 http://deb.debian.org/debian bookworm/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 143 http://deb.debian.org/debian bookworm/main i386 python3-iso8601 all 1.0.2-1 [15.7 kB]
Get: 144 http://deb.debian.org/debian bookworm/main i386 python3-more-itertools all 8.10.0-2 [53.0 kB]
Get: 145 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB]
Get: 146 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB]
Get: 147 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB]
Get: 148 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 149 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 150 http://deb.debian.org/debian bookworm/main i386 python3-pbcommand all 2.1.1+git20220616.3f2e6c2-2 [90.7 kB]
Get: 151 http://deb.debian.org/debian bookworm/main i386 python3-pysam i386 0.20.0+ds-3+b1 [1708 kB]
Get: 152 http://deb.debian.org/debian bookworm/main i386 python3-pbcore all 2.1.2+dfsg-5 [2830 kB]
Get: 153 http://deb.debian.org/debian bookworm/main i386 python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get: 154 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB]
Get: 155 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB]
Get: 156 http://deb.debian.org/debian bookworm/main i386 python3-pytest all 7.2.1-2 [236 kB]
Get: 157 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB]
Get: 158 http://deb.debian.org/debian bookworm/main i386 python3-pytest-runner all 2.11.1-4 [8432 B]
Get: 159 http://deb.debian.org/debian bookworm/main i386 python3-pytest-xdist all 3.1.0-1 [39.6 kB]
Get: 160 http://deb.debian.org/debian bookworm/main i386 python3-pythran i386 0.11.0+ds-7 [427 kB]
Get: 161 http://deb.debian.org/debian bookworm/main i386 python3-scipy i386 1.10.1-2 [15.2 MB]
Get: 162 http://deb.debian.org/debian bookworm/main i386 python3-uritools all 4.0.0-1 [25.3 kB]
Fetched 112 MB in 4s (26.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:i386.
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Setting up python3-minimal (3.11.2-1+b1) ...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_source.changes
dpkg-buildpackage: info: source package kineticstools
dpkg-buildpackage: info: source version 0.6.1+git20220223.1326a4d+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg'
dh_auto_clean
I: pybuild base:240: python3.11 setup.py clean
running clean
removing '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build' (and everything under it)
'build/bdist.linux-i386' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
rm -rf .pytest_cache
rm -rf kineticsTools.egg-info
rm -f nosetests.xml
rm -f bin/ipdSummary
make[1]: Leaving directory '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/pipelineTools.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/ResultWriter.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/MedakaLdaEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/MixtureEstimationMethods.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/ModificationDecode.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/WorkerProcess.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/ReferenceUtils.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/BasicLdaEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/loader.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteDetection.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/sharedArray.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/ipdSummary.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/KineticWorker.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/summarizeModifications.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteCommon.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/ipdModel.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
copying kineticsTools/PositiveControlEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/internal
copying kineticsTools/internal/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/internal
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/gather_bigwig.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks
running egg_info
creating kineticsTools.egg-info
writing kineticsTools.egg-info/PKG-INFO
writing dependency_links to kineticsTools.egg-info/dependency_links.txt
writing entry points to kineticsTools.egg-info/entry_points.txt
writing requirements to kineticsTools.egg-info/requires.txt
writing top-level names to kineticsTools.egg-info/top_level.txt
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSES.txt'
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kineticsTools.resources' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'kineticsTools.resources' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'kineticsTools.resources' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'kineticsTools.resources' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/P6-C4.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/SP2-C2.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/SP3-C3.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/unknown.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources
running build_ext
building 'kineticsTools/tree_predict' extension
creating build
creating build/temp.linux-i386-cpython-311
creating build/temp.linux-i386-cpython-311/kineticsTools
i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c kineticsTools/tree_predict.c -o build/temp.linux-i386-cpython-311/kineticsTools/tree_predict.o -O3 -shared -std=c99
i686-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/kineticsTools/tree_predict.o -L/usr/lib/i386-linux-gnu -o /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tree_predict.cpython-311-i386-linux-gnu.so
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg'
cp kineticsTools/ipdSummary.py bin/ipdSummary
chmod +x bin/ipdSummary
PYTHONPATH=/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg PATH=$PATH:/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/bin dh_auto_test
I: pybuild base:240: cd /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build; python3.11 -m pytest test
============================= test session starts ==============================
platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack -- /usr/bin/python3.11
cachedir: .pytest_cache
rootdir: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg, configfile: pytest.ini
plugins: xdist-3.1.0
gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I / gw8 I / gw9 I
[gw0] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw1] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw2] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw3] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw4] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw5] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw6] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw7] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw8] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw9] linux Python 3.11.2 cwd: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build
[gw0] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw1] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw3] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw2] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw4] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw5] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw6] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw7] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw8] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
[gw9] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0]
gw0 [19] / gw1 [19] / gw2 [19] / gw3 [19] / gw4 [19] / gw5 [19] / gw6 [19] / gw7 [19] / gw8 [19] / gw9 [19]
scheduling tests via LoadScopeScheduling
test/test_summarize_modifications.py::TestSummarizeModifications::test_integration
[gw6] [ 5%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration
test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig
[gw1] [ 10%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig
test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli
[gw1] [ 15%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli
test/test_outputs.py::TestOutputs::test_csv_output
[gw5] [ 21%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output
test/test_outputs.py::TestOutputs::test_bigwig
[gw5] [ 26%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig
test/test_ReferenceUtils.py::TestReferenceUtils::test_bam
[gw0] [ 31%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam
test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset
[gw0] [ 36%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset
test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow
[gw0] [ 42%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow
test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows
[gw0] [ 47%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows
test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks
test/test_ipdModel.py::TestIpdModel::test_refLength
[gw2] [ 52%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength
test/test_ipdModel.py::TestIpdModel::test_snippetFunc
[gw2] [ 57%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc
test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow
[gw2] [ 63%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow
[gw0] [ 68%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks
test/test_integration.py::TestKineticsTools::test_help
test/test_loader.py::test_basic
[gw4] [ 73%] PASSED test/test_loader.py::test_basic
test/test_loader.py::test_path
[gw4] [ 78%] PASSED test/test_loader.py::test_path
test/test_loader.py::test_path_with_prefixed_chem
[gw4] [ 84%] PASSED test/test_loader.py::test_path_with_prefixed_chem
test/test_loader.py::test_getResourcePathSpec
[gw4] [ 89%] PASSED test/test_loader.py::test_getResourcePathSpec
[gw3] [ 94%] PASSED test/test_integration.py::TestKineticsTools::test_help
test/test_integration.py::TestKineticsTools::test_ecoli_first_50k
[gw3] [100%] SKIPPED test/test_integration.py::TestKineticsTools::test_ecoli_first_50k
- generated xml file: /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/nosetests.xml -
============================= slowest 20 durations =============================
1.56s call .pybuild/cpython3_3.11_kineticstools/build/test/test_integration.py::TestKineticsTools::test_help
(19 durations < 0.005s hidden. Use -vv to show these durations.)
======================== 5 passed, 14 skipped in 4.70s =========================
make[1]: Leaving directory '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg'
create-stamp debian/debhelper-build-stamp
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+git20220223.1326a4d+dfsg'
dh_auto_install
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running egg_info
writing kineticsTools.egg-info/PKG-INFO
writing dependency_links to kineticsTools.egg-info/dependency_links.txt
writing entry points to kineticsTools.egg-info/entry_points.txt
writing requirements to kineticsTools.egg-info/requires.txt
writing top-level names to kineticsTools.egg-info/top_level.txt
reading manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSES.txt'
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'kineticsTools.resources' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'kineticsTools.resources' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'kineticsTools.resources' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'kineticsTools.resources' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
running build_ext
running install_lib
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/nosetests.xml -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/pipelineTools.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/ResultWriter.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/MedakaLdaEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/MixtureEstimationMethods.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tree_predict.cpython-311-i386-linux-gnu.so -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/internal
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/internal/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/internal
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/ModificationDecode.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/resources
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources/P6-C4.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/resources
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources/SP3-C3.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/resources
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources/unknown.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/resources
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/resources/SP2-C2.npz.gz -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/resources
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/WorkerProcess.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/ReferenceUtils.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/BasicLdaEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/loader.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/MultiSiteDetection.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/sharedArray.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/ipdSummary.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/KineticWorker.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/summarizeModifications.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/MultiSiteCommon.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/ipdModel.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/PositiveControlEnricher.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/__init__.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/loader.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/sharedArray.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/__pycache__/ReferenceUtils.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__pycache__
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks/gather_bigwig.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks/__init__.py -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks
creating /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks/__pycache__/gather_bigwig.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks/__pycache__
copying /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/.pybuild/cpython3_3.11_kineticstools/build/kineticsTools/tasks/__pycache__/__init__.cpython-311.pyc -> /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks/__pycache__
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/internal/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/loader.py to loader.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/sharedArray.py to sharedArray.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/ipdModel.py to ipdModel.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks/gather_bigwig.py to gather_bigwig.cpython-311.pyc
byte-compiling /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools/tasks/__init__.py to __init__.cpython-311.pyc
running install_egg_info
Copying kineticsTools.egg-info to /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/lib/python3.11/dist-packages/kineticsTools-0.8.0.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ipdSummary script to /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/bin
Installing summarizeModifications script to /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/python3-kineticstools/usr/bin
mkdir -p /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools/usr/bin
mv debian/python3-kineticstools/usr/bin/* /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools/usr/bin
mkdir -p /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools/usr/share/man//man1
rst2man doc/manual.rst > /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools/usr/share/man//man1/ipdSummary.1
doc/manual.rst:53: (WARNING/2) "math" role not supported
doc/manual.rst:55: (WARNING/2) "math" role not supported
doc/manual.rst:55: (WARNING/2) "math" role not supported
mkdir -p debian/kineticstools-data/usr/share/kineticstools
# There is probably a simpler way, but that should do for the moment.
set -e \
; for libdir in debian/python3-kineticstools/usr/lib/python3.* \
; do rm -rf /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools-data/usr/share/kineticstools/resources \
; mv ${libdir}/dist-packages/kineticsTools/resources /build/kineticstools-0.6.1+git20220223.1326a4d+dfsg/debian/kineticstools-data/usr/share/kineticstools/resources \
; done
rm debian/python3-kineticstools/usr/lib/python3.*/dist-packages/nosetests.xml
make[1]: Leaving directory '/build/kineticstools-0.6.1+git20220223.1326a4d+dfsg'
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
dh_installexamples -O--buildsystem=pybuild
dh_installman -O--buildsystem=pybuild
dh_python3 -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 -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
dh_gencontrol -O--buildsystem=pybuild
dpkg-gencontrol: warning: Depends field of package python3-kineticstools: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package python3-kineticstools: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'kineticstools' in '../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_all.deb'.
dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb'.
dpkg-deb: building package 'python3-kineticstools' in '../python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb'.
dpkg-deb: building package 'kineticstools-data' in '../kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb'.
dpkg-genbuildinfo --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo
dpkg-genchanges --build=binary -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/30953 and its subdirectories
I: Current time: Thu May 4 03:34:07 -12 2023
I: pbuilder-time-stamp: 1683214447
Thu May 4 15:34:08 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net.
Thu May 4 15:34:09 UTC 2023 I: Preparing to do remote build '2' on ionos16-i386.debian.net.
Thu May 4 15:35:55 UTC 2023 I: Deleting $TMPDIR on ionos16-i386.debian.net.
Thu May 4 15:35:55 UTC 2023 I: kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.changes:
Format: 1.8
Date: Wed, 21 Dec 2022 19:59:38 +0530
Source: kineticstools
Binary: kineticstools kineticstools-data python3-kineticstools python3-kineticstools-dbgsym
Architecture: all i386
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
kineticstools - detection of DNA modifications
kineticstools-data - detection of DNA modifications -- data files
python3-kineticstools - detection of DNA modifications (Python 3 library)
Closes: 1026742
Changes:
kineticstools (0.6.1+git20220223.1326a4d+dfsg-2) unstable; urgency=medium
.
* Team Upload.
* Test only for default python version as pysam is not
available for python3.11 (Closes: #1026742)
Checksums-Sha1:
3427c408fbe30787a88c86ddb3c1db7341edb40a 21693392 kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
b54f480248f4634ecc5d56d86c23aca3dd123fd5 14556 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
bc6107a91ced034f4fee6a572dd54ef72187042c 10391 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo
c32a1ef25aa79055d5b9f37aa8a5076cdbd25b98 5692 python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
e9690cc55f21d05eb78f024fbb9eca534389b2c3 46404 python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
Checksums-Sha256:
24f47d2a6eda6ce678101e1f740173430f7e5d89c4384f862f795f08b34ee231 21693392 kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
95b3d200e0d95115e43fa8421287f6d71c1be7b578deea41e827bdce3d30ba4e 14556 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
7021d5577f2671c54730bd3f64f2fe23460f3120439f53f98f15b46f22608fc6 10391 kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo
18f7639388a2f13ca0153cad0aa071cfdb8069f07437a5ed9d15711cd3d9f607 5692 python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
0fbd0466228e3ceb34b4bae99779307b0db385bfc6ccb79e124c250e8a8ab98a 46404 python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
Files:
d2ef3f4b0743d7931b972f13427c0545 21693392 science optional kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
d9fda0acd5bc055ebca4bb93b5a7a6be 14556 science optional kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_all.deb
83df67ae45192d9a0b2dfa7e2436ffe8 10391 science optional kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo
bff828c8dae9a989a73e2ac70a080dc4 5692 debug optional python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
0e12a993723207ee0a3dcc2b426447e2 46404 python optional python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.deb
Thu May 4 15:35:56 UTC 2023 I: diffoscope 241 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/b1/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.SnodrAFS/b2/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.584s)
0.584s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.240s)
0.240s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Thu May 4 15:35:58 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists.
Thu May 4 15:35:58 UTC 2023 I: kineticstools from bookworm built successfully and reproducibly on i386.
Thu May 4 15:35:59 UTC 2023 I: Submitting .buildinfo files to external archives:
Thu May 4 15:35:59 UTC 2023 I: Submitting 12K b1/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo.asc
Thu May 4 15:36:00 UTC 2023 I: Submitting 12K b2/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo.asc
Thu May 4 15:36:01 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu May 4 15:36:01 UTC 2023 I: Done submitting .buildinfo files.
Thu May 4 15:36:01 UTC 2023 I: Removing signed kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo.asc files:
removed './b1/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo.asc'
removed './b2/kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_i386.buildinfo.asc'