kineticstools →
0.6.1+git20220223.1326a4d+dfsg-2 →
armhf → 2022-12-27 05:10:27
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+========================================================================================+
| kineticstools 0.6.1+git20220223.1326a4d+dfsg-2 (armhf) Tue, 27 Dec 2022 04:48:33 +0000 |
+========================================================================================+
Package: kineticstools
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Source Version: 0.6.1+git20220223.1326a4d+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-6ff964ce-ff22-4b79-8a39-b4b98c61587f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/kineticstools-snKJzD/resolver-6h4Gxq' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.5 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.8 MB in 11s (2471 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'kineticstools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/kineticstools.git
Please use:
git clone https://salsa.debian.org/med-team/kineticstools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 21.8 MB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main kineticstools 0.6.1+git20220223.1326a4d+dfsg-2 (dsc) [2101 B]
Get:2 http://172.17.4.1/private bookworm-staging/main kineticstools 0.6.1+git20220223.1326a4d+dfsg-2 (tar) [21.8 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main kineticstools 0.6.1+git20220223.1326a4d+dfsg-2 (diff) [10.4 kB]
Fetched 21.8 MB in 3s (7295 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kineticstools-snKJzD/kineticstools-0.6.1+git20220223.1326a4d+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kineticstools-snKJzD' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-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, build-essential, fakeroot
Filtered Build-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, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [453 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [526 B]
Fetched 1936 B in 0s (50.8 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz file fonts-urw-base35 gettext gettext-base groff-base intltool-debian
libaec0 libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcurl3-gnutls
libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontenc1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-103-1
libhdf5-hl-100 libhts3 libhtscodecs2 libicu72 libimagequant0 libjbig0
libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmagic-mgc libmagic1 libmd0
libmpdec3 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16 libpsl5
libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
libpython3.11-minimal libpython3.11-stdlib libraqm0 librtmp1 libssh2-1
libsub-override-perl libsz2 libtiff5 libtool libuchardet0 libwebp7
libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap
man-db media-types mime-support openssl po-debconf python3 python3-attr
python3-avro python3-biopython python3-certifi python3-chardet
python3-charset-normalizer python3-decorator python3-distutils
python3-docutils python3-execnet python3-h5py python3-h5py-serial
python3-idna python3-iniconfig python3-iso8601 python3-lib2to3
python3-minimal python3-more-itertools python3-numpy python3-packaging
python3-pbcommand python3-pbcore python3-pil python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pysam python3-pytest
python3-pytest-runner python3-pytest-xdist python3-renderpm
python3-reportlab python3-reportlab-accel python3-requests python3-roman
python3-scipy python3-setuptools python3-six python3-tomli python3-tz
python3-uritools python3-urllib3 python3.10 python3.10-minimal python3.11
python3.11-minimal w3c-sgml-lib x11-common xfonts-encodings xfonts-utils
xml-core
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-installer fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre
gettext-doc libasprintf-dev libgettextpo-dev groff low-memory-monitor
liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss
fasttree mafft muscle phylip phyml prank probcons python3-mysqldb
python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 raxml
samtools t-coffee wise docutils-doc fonts-linuxlibertine
| ttf-linux-libertine texlive-lang-french texlive-latex-base
texlive-latex-recommended execnet-doc python-h5py-doc gfortran
python-numpy-doc python3-dev python-pbcore-doc python-pil-doc subversion
python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools
python-reportlab-doc python3-cryptography python3-openssl python3-socks
python-requests-doc python-scipy-doc python-setuptools-doc python3-brotli
python3.10-venv python3.10-doc binfmt-support python3.11-venv python3.11-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common publicsuffix libltdl-dev
libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils
python3-pygments python3-olefile
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
dwz file fonts-urw-base35 gettext gettext-base groff-base intltool-debian
libaec0 libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcurl3-gnutls
libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontenc1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhdf5-103-1
libhdf5-hl-100 libhts3 libhtscodecs2 libicu72 libimagequant0 libjbig0
libjpeg62-turbo libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libmagic-mgc libmagic1 libmd0
libmpdec3 libnghttp2-14 libopenjp2-7 libpipeline1 libpng16-16 libpsl5
libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
libpython3.11-minimal libpython3.11-stdlib libraqm0 librtmp1 libssh2-1
libsub-override-perl libsz2 libtiff5 libtool libuchardet0 libwebp7
libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 m4 mailcap
man-db media-types mime-support openssl po-debconf python3 python3-attr
python3-avro python3-biopython python3-certifi python3-chardet
python3-charset-normalizer python3-decorator python3-distutils
python3-docutils python3-execnet python3-h5py python3-h5py-serial
python3-idna python3-iniconfig python3-iso8601 python3-lib2to3
python3-minimal python3-more-itertools python3-numpy python3-packaging
python3-pbcommand python3-pbcore python3-pil python3-pkg-resources
python3-pluggy python3-py python3-pyparsing python3-pysam python3-pytest
python3-pytest-runner python3-pytest-xdist python3-renderpm
python3-reportlab python3-reportlab-accel python3-requests python3-roman
python3-scipy python3-setuptools python3-six python3-tomli python3-tz
python3-uritools python3-urllib3 python3.10 python3.10-minimal python3.11
python3.11-minimal sbuild-build-depends-main-dummy w3c-sgml-lib x11-common
xfonts-encodings xfonts-utils xml-core
0 upgraded, 143 newly installed, 0 to remove and 13 not upgraded.
Need to get 76.8 MB of archives.
After this operation, 304 MB of additional disk space will be used.
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Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.9-1 [769 kB]
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Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-3 [25.5 kB]
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Get:7 http://172.17.4.1/private bookworm-staging/main armhf mailcap all 3.70+nmu1 [32.0 kB]
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Get:16 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-9 [774 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-4 [78.8 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.1-1 [1341 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.7-1 [1349 kB]
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Get:23 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
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Get:25 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-10 [156 kB]
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Get:28 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-10 [495 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.11.3 [81.1 kB]
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Get:34 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-2 [8556 B]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [570 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-10 [1203 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
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Get:47 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
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Get:50 http://172.17.4.1/private bookworm-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf docutils-common all 0.17.1+dfsg-3 [113 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfontenc1 armhf 1:1.1.4-1 [22.3 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.39-2 [258 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf xfonts-encodings all 1:1.0.4-2.1 [573 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf xfonts-utils armhf 1:7.7+6 [82.5 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf fonts-urw-base35 all 20200910-6 [6374 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
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Get:65 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
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Get:68 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.86.0-2 [318 kB]
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Get:70 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
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Get:102 http://172.17.4.1/private bookworm-staging/main armhf python3-attr all 22.2.0-1 [65.4 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf python3-avro all 1.11.1+dfsg-1 [70.9 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf python3.11 armhf 3.11.1-1 [567 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.23.5-2+b1 [5285 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf python3-renderpm armhf 3.6.11-1 [69.9 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab-accel armhf 3.6.11-1 [41.3 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf python3-pil armhf 9.2.0-1.1 [427 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf python3-reportlab all 3.6.11-1 [566 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf w3c-sgml-lib all 1.3-3 [273 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf python3-biopython armhf 1.80+dfsg-1 [1568 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf python3-certifi all 2022.9.24-1 [153 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf python3-chardet all 4.0.0-2 [99.1 kB]
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Get:116 http://172.17.4.1/private bookworm-staging/main armhf python3-decorator all 5.1.1-3 [14.9 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf python3-roman all 3.3-3 [9880 B]
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Get:120 http://172.17.4.1/private bookworm-staging/main armhf python3-h5py-serial armhf 3.7.0-3 [710 kB]
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Get:125 http://172.17.4.1/private bookworm-staging/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf python3-pyparsing all 3.0.9-1 [138 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf python3-packaging all 21.3-1.1 [34.2 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf python3-urllib3 all 1.26.12-1 [117 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf python3-tz all 2022.7-1 [32.1 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf python3-pbcommand all 2.1.1+git20220616.3f2e6c2-2 [90.7 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf python3-pysam armhf 0.17.0+ds-2+b1 [1834 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf python3-pbcore all 2.1.2+dfsg-3 [2831 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf python3-py all 1.11.0-1 [89.2 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf python3-tomli all 2.0.1-2 [17.9 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest all 7.1.2-4 [218 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-runner all 2.11.1-4 [8432 B]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf python3-pytest-xdist all 3.1.0-1 [39.6 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf python3-scipy armhf 1.8.1-14+rpi1 [12.9 MB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf python3-uritools all 4.0.0-1 [25.3 kB]
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Setting up libhtscodecs2:armhf (1.3.0-4) ...
Setting up media-types (8.0.0) ...
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Setting up libgraphite2-3:armhf (1.3.14-1) ...
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Setting up libglib2.0-0:armhf (2.74.1-2) ...
No schema files found: doing nothing.
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Setting up libbrotli1:armhf (1.0.9-2+b2) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libnghttp2-14:armhf (1.51.0-1) ...
Setting up libmagic1:armhf (1:5.41-4) ...
Setting up libdeflate0:armhf (1.14-1) ...
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Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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Setting up libpng16-16:armhf (1.6.39-2) ...
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Setting up libxml2:armhf (2.9.14+dfsg-1.1) ...
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Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up liblapack3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
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Setting up libwebpdemux2:armhf (1.2.2-2+b1) ...
Setting up libpython3.11-stdlib:armhf (3.11.1-1) ...
Setting up libcurl3-gnutls:armhf (7.86.0-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libpython3.10-stdlib:armhf (3.10.9-1) ...
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Setting up ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
127 added, 0 removed; done.
Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libjs-sphinxdoc (5.3.0-2) ...
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Setting up libcurl4:armhf (7.86.0-2) ...
Setting up libharfbuzz0b:armhf (5.2.0-2+b1) ...
Setting up libpython3-stdlib:armhf (3.10.6-3) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.3-11) ...
Setting up python3.11 (3.11.1-1) ...
Setting up libhts3:armhf (1.16+ds-3) ...
Setting up python3.10 (3.10.9-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.10.6-3) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.11.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3-tz (2022.7-1) ...
Setting up python3-six (1.16.0-4) ...
Setting up python3-roman (3.3-3) ...
Setting up python3-decorator (5.1.1-3) ...
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Setting up python3-pyparsing (3.0.9-1) ...
Setting up python3-certifi (2022.9.24-1) ...
Setting up python3-avro (1.11.1+dfsg-1) ...
Setting up libraqm0:armhf (0.7.0-4) ...
Setting up python3-reportlab-accel:armhf (3.6.11-1) ...
Setting up python3-idna (3.3-1) ...
Setting up python3-urllib3 (1.26.12-1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up libhdf5-103-1:armhf (1.10.8+repack1-1) ...
Setting up python3-execnet (1.9.0-1) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up libhdf5-hl-100:armhf (1.10.8+repack1-1) ...
Setting up python3-uritools (4.0.0-1) ...
Setting up python3-pkg-resources (65.5.0-1) ...
Setting up python3-distutils (3.10.8-1) ...
Setting up dh-python (5.20220819+rpi1) ...
Setting up python3-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-attr (22.2.0-1) ...
Setting up python3-pysam (0.17.0+ds-2+b1) ...
Setting up python3-setuptools (65.5.0-1) ...
Setting up python3-tomli (2.0.1-2) ...
Setting up python3-py (1.11.0-1) ...
Setting up python3-charset-normalizer (3.0.1-2) ...
Setting up debhelper (13.11.3) ...
Setting up fonts-urw-base35 (20200910-6) ...
Setting up python3-pil:armhf (9.2.0-1.1) ...
Setting up python3-packaging (21.3-1.1) ...
Setting up python3-chardet (4.0.0-2) ...
Setting up python3-requests (2.28.1+dfsg-1) ...
Setting up python3-numpy (1:1.23.5-2+b1) ...
Setting up python3-reportlab (3.6.11-1) ...
Setting up python3-pytest-runner (2.11.1-4) ...
Setting up python3-scipy (1.8.1-14+rpi1) ...
Setting up python3-renderpm:armhf (3.6.11-1) ...
Setting up python3-pytest (7.1.2-4) ...
Setting up python3-h5py-serial (3.7.0-3) ...
Setting up python3-h5py (3.7.0-3) ...
Setting up python3-pbcommand (2.1.1+git20220616.3f2e6c2-2) ...
Setting up python3-pytest-xdist (3.1.0-1) ...
Processing triggers for libc-bin (2.36-6+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up docutils-common (0.17.1+dfsg-3) ...
Setting up python3-biopython (1.80+dfsg-1) ...
Setting up python3-pbcore (2.1.2+dfsg-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.17.1+dfsg-3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39.50.20221208-5+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-10+rpi1 gcc-12_12.2.0-10+rpi1 libc6-dev_2.36-6+rpi1 libstdc++-12-dev_12.2.0-10+rpi1 libstdc++6_12.2.0-10+rpi1 linux-libc-dev_6.0.12-1+rpi1
Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2-2 binutils_2.39.50.20221208-5+rpi1 binutils-arm-linux-gnueabihf_2.39.50.20221208-5+rpi1 binutils-common_2.39.50.20221208-5+rpi1 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dirmngr_2.2.40-1 docutils-common_0.17.1+dfsg-3 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fonts-urw-base35_20200910-6 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-10+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-10+rpi1 gcc-12-base_12.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----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:
c120e21be482516be94a44b19c1901e563ba1d2eef34af4273a219e78dcecbbd 21772620 kineticstools_0.6.1+git20220223.1326a4d+dfsg.orig.tar.xz
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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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ERRzpVo3/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 21 14:37:16 2022 UTC
gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./kineticstools_0.6.1+git20220223.1326a4d+dfsg-2.dsc
dpkg-source: info: extracting kineticstools in /<<PKGBUILDDIR>>
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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=f6531457acff44088f965ef4ced20cd2
JOURNAL_STREAM=8:31902
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-6ff964ce-ff22-4b79-8a39-b4b98c61587f
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c11961
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
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-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:240: python3.10 setup.py clean
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.10' 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 '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_autoreconf -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:240: python3.10 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/BasicLdaEnricher.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/KineticWorker.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/MedakaLdaEnricher.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/MixtureEstimationMethods.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/ModificationDecode.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteCommon.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteDetection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/PositiveControlEnricher.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/ReferenceUtils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/ResultWriter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/WorkerProcess.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/ipdModel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/ipdSummary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/loader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/pipelineTools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/sharedArray.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
copying kineticsTools/summarizeModifications.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/internal
copying kineticsTools/internal/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/internal
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/gather_bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_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 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/P6-C4.npz.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/SP2-C2.npz.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/SP3-C3.npz.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/unknown.npz.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources
running build_ext
building 'kineticsTools/tree_predict' extension
creating build
creating build/temp.linux-armhf-cpython-310
creating build/temp.linux-armhf-cpython-310/kineticsTools
arm-linux-gnueabihf-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c kineticsTools/tree_predict.c -o build/temp.linux-armhf-cpython-310/kineticsTools/tree_predict.o -O3 -shared -std=c99
arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-310/kineticsTools/tree_predict.o -L/usr/lib/arm-linux-gnueabihf -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tree_predict.cpython-310-arm-linux-gnueabihf.so
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp kineticsTools/ipdSummary.py bin/ipdSummary
chmod +x bin/ipdSummary
PYTHONPATH=/<<PKGBUILDDIR>> PATH=$PATH:/<<PKGBUILDDIR>>/bin dh_auto_test
I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build; python3.10 -m pytest test
============================= test session starts ==============================
platform linux -- Python 3.10.9, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.10
cachedir: .pytest_cache
rootdir: /<<PKGBUILDDIR>>, configfile: pytest.ini
plugins: xdist-3.1.0
gw0 I / gw1 I / gw2 I / gw3 I
[gw0] linux Python 3.10.9 cwd: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build
[gw1] linux Python 3.10.9 cwd: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build
[gw2] linux Python 3.10.9 cwd: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build
[gw3] linux Python 3.10.9 cwd: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build
[gw0] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0]
[gw1] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0]
[gw2] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0]
[gw3] Python 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0]
gw0 [19] / gw1 [19] / gw2 [19] / gw3 [19]
scheduling tests via LoadScopeScheduling
test/test_ReferenceUtils.py::TestReferenceUtils::test_bam
test/test_ipdModel.py::TestIpdModel::test_refLength
[gw0] [ 5%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_bam
test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset
[gw0] [ 10%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_dataset
test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow
test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig
[gw1] [ 15%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig
test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli
[gw1] [ 21%] SKIPPED test/test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli
test/test_loader.py::test_basic
[gw1] [ 26%] PASSED test/test_loader.py::test_basic
[gw0] [ 31%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow
test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows
[gw0] [ 36%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows
test/test_integration.py::TestKineticsTools::test_help
test/test_loader.py::test_path
[gw3] [ 42%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_refLength
[gw1] [ 47%] PASSED test/test_loader.py::test_path
test/test_loader.py::test_path_with_prefixed_chem
[gw1] [ 52%] PASSED test/test_loader.py::test_path_with_prefixed_chem
test/test_ipdModel.py::TestIpdModel::test_snippetFunc
[gw3] [ 57%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_snippetFunc
test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks
[gw0] [ 63%] SKIPPED test/test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks
test/test_summarize_modifications.py::TestSummarizeModifications::test_integration
[gw0] [ 68%] SKIPPED test/test_summarize_modifications.py::TestSummarizeModifications::test_integration
test/test_loader.py::test_getResourcePathSpec
[gw1] [ 73%] PASSED test/test_loader.py::test_getResourcePathSpec
test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow
[gw3] [ 78%] SKIPPED test/test_ipdModel.py::TestIpdModel::test_getReferenceWindow
[gw2] [ 84%] PASSED test/test_integration.py::TestKineticsTools::test_help
test/test_integration.py::TestKineticsTools::test_ecoli_first_50k
[gw2] [ 89%] SKIPPED test/test_integration.py::TestKineticsTools::test_ecoli_first_50k
test/test_outputs.py::TestOutputs::test_csv_output
[gw2] [ 94%] SKIPPED test/test_outputs.py::TestOutputs::test_csv_output
test/test_outputs.py::TestOutputs::test_bigwig
[gw2] [100%] SKIPPED test/test_outputs.py::TestOutputs::test_bigwig
- generated xml file: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/nosetests.xml -
============================= slowest 20 durations =============================
1.89s call .pybuild/cpython3_3.10_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 4.66s =========================
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
I: pybuild base:240: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/python3-kineticstools
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/BasicLdaEnricher.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/KineticWorker.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/MedakaLdaEnricher.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/MixtureEstimationMethods.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/ModificationDecode.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/MultiSiteCommon.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/MultiSiteDetection.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/PositiveControlEnricher.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/ReferenceUtils.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/ResultWriter.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/WorkerProcess.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/ipdModel.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/ipdSummary.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/loader.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/pipelineTools.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/sharedArray.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/summarizeModifications.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/internal
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/internal/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/internal
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks/gather_bigwig.py -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks/__pycache__/__init__.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tasks/__pycache__/gather_bigwig.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks/__pycache__
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/resources
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources/P6-C4.npz.gz -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/resources
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources/SP2-C2.npz.gz -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/resources
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources/SP3-C3.npz.gz -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/resources
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/resources/unknown.npz.gz -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/resources
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/tree_predict.cpython-310-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools
creating /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__pycache__/__init__.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__pycache__/ReferenceUtils.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__pycache__/ipdModel.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__pycache__/sharedArray.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/kineticsTools/__pycache__/loader.cpython-310.pyc -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_kineticstools/build/nosetests.xml -> /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/__init__.py to __init__.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/ipdModel.py to ipdModel.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/loader.py to loader.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/sharedArray.py to sharedArray.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/internal/__init__.py to __init__.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks/__init__.py to __init__.cpython-310.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools/tasks/gather_bigwig.py to gather_bigwig.cpython-310.pyc
running install_egg_info
Copying kineticsTools.egg-info to /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/lib/python3.10/dist-packages/kineticsTools-0.8.0.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ipdSummary script to /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/bin
Installing summarizeModifications script to /<<PKGBUILDDIR>>/debian/python3-kineticstools/usr/bin
mkdir -p /<<PKGBUILDDIR>>/debian/kineticstools/usr/bin
mv debian/python3-kineticstools/usr/bin/* /<<PKGBUILDDIR>>/debian/kineticstools/usr/bin
mkdir -p /<<PKGBUILDDIR>>/debian/kineticstools/usr/share/man//man1
rst2man doc/manual.rst > /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/debian/kineticstools-data/usr/share/kineticstools/resources \
; mv ${libdir}/dist-packages/kineticsTools/resources /<<PKGBUILDDIR>>/debian/kineticstools-data/usr/share/kineticstools/resources \
; done
rm debian/python3-kineticstools/usr/lib/python3.*/dist-packages/nosetests.xml
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_installexamples -a -O--buildsystem=pybuild
dh_installman -a -O--buildsystem=pybuild
dh_python3 -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -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 -a -O--buildsystem=pybuild
dh_gencontrol -a -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 -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-kineticstools-dbgsym' in '../python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb'.
dpkg-deb: building package 'python3-kineticstools' in '../python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-12-27T05:10:20Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.changes:
-------------------------------------------------------------
Format: 1.8
Date: Wed, 21 Dec 2022 19:59:38 +0530
Source: kineticstools
Binary: python3-kineticstools python3-kineticstools-dbgsym
Architecture: armhf
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
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:
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Files:
f666f41f4d29d450d91749752c5e6b63 9187 science optional kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.buildinfo
ce94fc95423d419a00e431ff4272caaf 5984 debug optional python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb
5c833aa1c571e09fcdab5ce82a08ebd5 46276 python optional python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: kineticstools
Binary: python3-kineticstools python3-kineticstools-dbgsym
Architecture: armhf
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Checksums-Md5:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 27 Dec 2022 05:10:19 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-10),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2-2),
binutils (= 2.39.50.20221208-5+rpi1),
binutils-arm-linux-gnueabihf (= 2.39.50.20221208-5+rpi1),
binutils-common (= 2.39.50.20221208-5+rpi1),
bsdextrautils (= 2.38.1-4),
bsdutils (= 1:2.38.1-4),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
ca-certificates (= 20211016),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-10+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.80),
debhelper (= 13.11.3),
debianutils (= 5.7-0.4),
dh-autoreconf (= 20),
dh-python (= 5.20220819+rpi1),
dh-strip-nondeterminism (= 1.13.0-2),
diffutils (= 1:3.8-1),
docutils-common (= 0.17.1+dfsg-3),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
fonts-urw-base35 (= 20200910-6),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-10+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-10+rpi1),
gcc-12-base (= 12.2.0-10+rpi1),
gettext (= 0.21-10),
gettext-base (= 0.21-10),
grep (= 3.8-3),
groff-base (= 1.22.4-9),
gzip (= 1.12-1),
hostname (= 3.23),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-2),
libaec0 (= 1.0.6-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-10+rpi1),
libatomic1 (= 12.2.0-10+rpi1),
libattr1 (= 1:2.5.1-3),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39.50.20221208-5+rpi1),
libblas3 (= 3.10.1-2),
libblkid1 (= 2.38.1-4),
libbrotli1 (= 1.0.9-2+b2),
libbsd0 (= 0.11.7-1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.36-6+rpi1),
libc-dev-bin (= 2.36-6+rpi1),
libc6 (= 2.36-6+rpi1),
libc6-dev (= 2.36-6+rpi1),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 12.2.0-10+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.33-1),
libcrypt1 (= 1:4.4.33-1),
libctf-nobfd0 (= 2.39.50.20221208-5+rpi1),
libctf0 (= 2.39.50.20221208-5+rpi1),
libcurl3-gnutls (= 7.86.0-2),
libcurl4 (= 7.86.0-2),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.265),
libdebhelper-perl (= 13.11.3),
libdeflate0 (= 1.14-1),
libdpkg-perl (= 1.21.9+rpi1),
libelf1 (= 0.187-2+rpi2),
libexpat1 (= 2.5.0-1),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.0-2),
libfontenc1 (= 1:1.1.4-1),
libfreetype6 (= 2.12.1+dfsg-3),
libfribidi0 (= 1.0.8-2.1),
libgcc-12-dev (= 12.2.0-10+rpi1),
libgcc-s1 (= 12.2.0-10+rpi1),
libgcrypt20 (= 1.10.1-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran5 (= 12.2.0-10+rpi1),
libglib2.0-0 (= 2.74.1-2),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgnutls30 (= 3.7.8-4),
libgomp1 (= 12.2.0-10+rpi1),
libgpg-error0 (= 1.46-1),
libgraphite2-3 (= 1.3.14-1),
libgssapi-krb5-2 (= 1.20.1-1),
libharfbuzz0b (= 5.2.0-2+b1),
libhdf5-103-1 (= 1.10.8+repack1-1),
libhdf5-hl-100 (= 1.10.8+repack1-1),
libhogweed6 (= 3.8.1-2),
libhts3 (= 1.16+ds-3),
libhtscodecs2 (= 1.3.0-4),
libicu72 (= 72.1-3),
libidn2-0 (= 2.3.3-1),
libimagequant0 (= 2.17.0-1),
libisl23 (= 0.25-1),
libjansson4 (= 2.14-2),
libjbig0 (= 2.1-6.1),
libjpeg62-turbo (= 1:2.1.2-1),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-sphinxdoc (= 5.3.0-2),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-2),
libk5crypto3 (= 1.20.1-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20.1-1),
libkrb5support0 (= 1.20.1-1),
liblapack3 (= 3.10.1-2),
liblbfgsb0 (= 3.0+dfsg.3-11),
liblcms2-2 (= 2.13.1-1),
libldap-2.5-0 (= 2.5.13+dfsg-2+rpi1+b1),
liblerc4 (= 4.0.0+ds-2),
liblz4-1 (= 1.9.4-1+rpi1),
liblzf1 (= 3.6-3),
liblzma5 (= 5.4.0-0.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-4),
libmpc3 (= 1.2.1-2),
libmpdec3 (= 2.5.1-2+rpi1),
libmpfr6 (= 4.1.0-3),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.8.1-2),
libnghttp2-14 (= 1.51.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libopenjp2-7 (= 2.5.0-1),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpcre2-8-0 (= 10.40-3),
libperl5.36 (= 5.36.0-6),
libpipeline1 (= 1.5.7-1),
libpng16-16 (= 1.6.39-2),
libpsl5 (= 0.21.0-1.2),
libpython3-stdlib (= 3.10.6-3),
libpython3.10-minimal (= 3.10.9-1),
libpython3.10-stdlib (= 3.10.9-1),
libpython3.11-minimal (= 3.11.1-1),
libpython3.11-stdlib (= 3.11.1-1),
libraqm0 (= 0.7.0-4),
libreadline8 (= 8.2-1.2),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg-10),
libsasl2-modules-db (= 2.1.28+dfsg-10),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsmartcols1 (= 2.38.1-4),
libsqlite3-0 (= 3.40.0-1),
libssh2-1 (= 1.10.0-3+b1),
libssl3 (= 3.0.7-1),
libstdc++-12-dev (= 12.2.0-10+rpi1),
libstdc++6 (= 12.2.0-10+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 252.2-1+rpi1),
libsz2 (= 1.0.6-1),
libtasn1-6 (= 4.19.0-2),
libtiff5 (= 4.4.0-6),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-5),
libubsan1 (= 12.2.0-10+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 252.2-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-4),
libwebp7 (= 1.2.2-2+b1),
libwebpdemux2 (= 1.2.2-2+b1),
libwebpmux3 (= 1.2.2-2+b1),
libxau6 (= 1:1.0.9-1),
libxcb1 (= 1.15-1),
libxdmcp6 (= 1:1.1.2-3),
libxml2 (= 2.9.14+dfsg-1.1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 6.0.12-1+rpi1),
login (= 1:4.13+dfsg1-1),
lsb-base (= 11.4+rpi1),
m4 (= 1.4.19-1),
mailcap (= 3.70+nmu1),
make (= 4.3-4.1),
man-db (= 2.11.1-1),
mawk (= 1.3.4.20200120-3.1),
media-types (= 8.0.0),
mime-support (= 3.66),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
openssl (= 3.0.7-1),
patch (= 2.7.6-7),
perl (= 5.36.0-6),
perl-base (= 5.36.0-6),
perl-modules-5.36 (= 5.36.0-6),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.10.6-3),
python3-attr (= 22.2.0-1),
python3-avro (= 1.11.1+dfsg-1),
python3-biopython (= 1.80+dfsg-1),
python3-certifi (= 2022.9.24-1),
python3-chardet (= 4.0.0-2),
python3-charset-normalizer (= 3.0.1-2),
python3-decorator (= 5.1.1-3),
python3-distutils (= 3.10.8-1),
python3-docutils (= 0.17.1+dfsg-3),
python3-execnet (= 1.9.0-1),
python3-h5py (= 3.7.0-3),
python3-h5py-serial (= 3.7.0-3),
python3-idna (= 3.3-1),
python3-iniconfig (= 1.1.1-2),
python3-iso8601 (= 1.0.2-1),
python3-lib2to3 (= 3.10.8-1),
python3-minimal (= 3.10.6-3),
python3-more-itertools (= 8.10.0-2),
python3-numpy (= 1:1.23.5-2+b1),
python3-packaging (= 21.3-1.1),
python3-pbcommand (= 2.1.1+git20220616.3f2e6c2-2),
python3-pbcore (= 2.1.2+dfsg-3),
python3-pil (= 9.2.0-1.1),
python3-pkg-resources (= 65.5.0-1),
python3-pluggy (= 1.0.0+repack-1),
python3-py (= 1.11.0-1),
python3-pyparsing (= 3.0.9-1),
python3-pysam (= 0.17.0+ds-2+b1),
python3-pytest (= 7.1.2-4),
python3-pytest-runner (= 2.11.1-4),
python3-pytest-xdist (= 3.1.0-1),
python3-renderpm (= 3.6.11-1),
python3-reportlab (= 3.6.11-1),
python3-reportlab-accel (= 3.6.11-1),
python3-requests (= 2.28.1+dfsg-1),
python3-roman (= 3.3-3),
python3-scipy (= 1.8.1-14+rpi1),
python3-setuptools (= 65.5.0-1),
python3-six (= 1.16.0-4),
python3-tomli (= 2.0.1-2),
python3-tz (= 2022.7-1),
python3-uritools (= 4.0.0-1),
python3-urllib3 (= 1.26.12-1),
python3.10 (= 3.10.9-1),
python3.10-minimal (= 3.10.9-1),
python3.11 (= 3.11.1-1),
python3.11-minimal (= 3.11.1-1),
readline-common (= 8.2-1.2),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysvinit-utils (= 3.05-7),
tar (= 1.34+dfsg-1),
tzdata (= 2022f-1),
util-linux (= 2.38.1-4),
util-linux-extra (= 2.38.1-4),
w3c-sgml-lib (= 1.3-3),
x11-common (= 1:7.7+23),
xfonts-encodings (= 1:1.0.4-2.1),
xfonts-utils (= 1:7.7+6),
xml-core (= 0.18+nmu1),
xz-utils (= 5.4.0-0.1),
zlib1g (= 1:1.2.13.dfsg-1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1671632978"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python3-kineticstools-dbgsym_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb
-----------------------------------------------------------------------
new Debian package, version 2.0.
size 5984 bytes: control archive=564 bytes.
467 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: python3-kineticstools-dbgsym
Source: kineticstools
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18
Depends: python3-kineticstools (= 0.6.1+git20220223.1326a4d+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for python3-kineticstools
Build-Ids: af343838f40829f2bd03853721d63e4979369386
drwxr-xr-x root/root 0 2022-12-21 14:29 ./
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/debug/.build-id/af/
-rw-r--r-- root/root 7468 2022-12-21 14:29 ./usr/lib/debug/.build-id/af/343838f40829f2bd03853721d63e4979369386.debug
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/share/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-12-21 14:29 ./usr/share/doc/python3-kineticstools-dbgsym -> python3-kineticstools
python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2_armhf.deb
----------------------------------------------------------------
new Debian package, version 2.0.
size 46276 bytes: control archive=2104 bytes.
1072 bytes, 20 lines control
3057 bytes, 31 lines md5sums
289 bytes, 12 lines * postinst #!/bin/sh
402 bytes, 12 lines * prerm #!/bin/sh
Package: python3-kineticstools
Source: kineticstools
Version: 0.6.1+git20220223.1326a4d+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 275
Depends: python3 (<< 3.11), python3 (>= 3.10~), python3-numpy, python3-pbcommand, python3-pbcore, python3-pybigwig, python3-scipy, python3:any, kineticstools-data (= 0.6.1+git20220223.1326a4d+dfsg-2)
Section: python
Priority: optional
Homepage: https://github.com/PacificBiosciences/kineticsTools
Description: detection of DNA modifications (Python 3 library)
Tools for detecting DNA modifications from single molecule, real-time (SMRT®)
sequencing data. This tool implements the P_ModificationDetection module in
SMRT® Portal, used by the RS_Modification_Detection and
RS_Modifications_and_Motif_Detection protocol. Researchers interested in
understanding or extending the modification detection algorithms can use these
tools as a starting point.
.
This package is part of the SMRTAnalysis suite and contains the backend
Python 3 library.
drwxr-xr-x root/root 0 2022-12-21 14:29 ./
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-rw-r--r-- root/root 2762 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/BasicLdaEnricher.py
-rw-r--r-- root/root 34458 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/KineticWorker.py
-rw-r--r-- root/root 3700 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/MedakaLdaEnricher.py
-rw-r--r-- root/root 11113 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/MixtureEstimationMethods.py
-rw-r--r-- root/root 14350 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/ModificationDecode.py
-rw-r--r-- root/root 5158 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/MultiSiteCommon.py
-rw-r--r-- root/root 9748 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/MultiSiteDetection.py
-rw-r--r-- root/root 5190 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/PositiveControlEnricher.py
-rw-r--r-- root/root 4365 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/ReferenceUtils.py
-rw-r--r-- root/root 20650 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/ResultWriter.py
-rw-r--r-- root/root 6096 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/WorkerProcess.py
-rw-r--r-- root/root 0 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/__init__.py
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/python3/dist-packages/kineticsTools/internal/
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-rw-r--r-- root/root 20039 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/ipdModel.py
-rw-r--r-- root/root 23827 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/ipdSummary.py
-rw-r--r-- root/root 2118 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/loader.py
-rw-r--r-- root/root 350 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/pipelineTools.py
lrwxrwxrwx root/root 0 2022-12-21 14:29 ./usr/lib/python3/dist-packages/kineticsTools/resources -> ../../../../share/kineticstools/resources
-rw-r--r-- root/root 569 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/sharedArray.py
-rw-r--r-- root/root 5951 2022-02-23 23:24 ./usr/lib/python3/dist-packages/kineticsTools/summarizeModifications.py
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/lib/python3/dist-packages/kineticsTools/tasks/
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drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-12-21 14:29 ./usr/share/doc/python3-kineticstools/
-rw-r--r-- root/root 1617 2022-12-21 14:29 ./usr/share/doc/python3-kineticstools/changelog.Debian.gz
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-rw-r--r-- root/root 2082 2022-12-21 14:24 ./usr/share/doc/python3-kineticstools/copyright
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 65928
Build-Time: 31
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1235
Job: kineticstools_0.6.1+git20220223.1326a4d+dfsg-2
Machine Architecture: armhf
Package: kineticstools
Package-Time: 1307
Source-Version: 0.6.1+git20220223.1326a4d+dfsg-2
Space: 65928
Status: successful
Version: 0.6.1+git20220223.1326a4d+dfsg-2
--------------------------------------------------------------------------------
Finished at 2022-12-27T05:10:20Z
Build needed 00:21:47, 65928k disk space