kineticstools →
0.6.1+git20180425.27a1878-2 →
armhf → 2019-02-24 05:01:05
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
Negative repeat count does nothing at /usr/share/perl5/Sbuild/Build.pm line 2740.
+==============================================================================+
Negative repeat count does nothing at /usr/share/perl5/Sbuild/Base.pm line 124.
| kineticstools 0.6.1+git20180425.27a1878-2 (armhf) Sun, 24 Feb 2019 04:45:04 +0000 |
+==============================================================================+
Package: kineticstools
Version: 0.6.1+git20180425.27a1878-2
Source Version: 0.6.1+git20180425.27a1878-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-c5ffed34-aab0-4849-9090-9004f5515dda' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 26s (935 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 110 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main kineticstools 0.6.1+git20180425.27a1878-2 (dsc) [2556 B]
Get:2 http://172.17.0.1/private buster-staging/main kineticstools 0.6.1+git20180425.27a1878-2 (tar) [110 MB]
Get:3 http://172.17.0.1/private buster-staging/main kineticstools 0.6.1+git20180425.27a1878-2 (diff) [8248 B]
Fetched 110 MB in 11s (10.4 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kineticstools-tU9rDX/kineticstools-0.6.1+git20180425.27a1878' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kineticstools-tU9rDX' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-HxdFYD/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-HxdFYD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-HxdFYD/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3110 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-HxdFYD/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core 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:
ca-certificates e2fsprogs-l10n krb5-locales libgpg-error-l10n
libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (20.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15640 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy, python-h5py, python-scipy, python-pytest
Filtered Build-Depends: debhelper (>= 12~), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy, python-h5py, python-scipy, python-pytest
dpkg-deb: building package 'sbuild-build-depends-kineticstools-dummy' in '/<<BUILDDIR>>/resolver-HxdFYD/apt_archive/sbuild-build-depends-kineticstools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-kineticstools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Sources [564 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Packages [644 B]
Fetched 2541 B in 1s (3674 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-HxdFYD/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install kineticstools 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:
e2fsprogs-l10n krb5-locales libgpg-error-l10n libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file
gettext gettext-base groff-base intltool-debian libaec0 libarchive-zip-perl
libblas3 libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103
libhts2 libicu63 liblapack3 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libsz2 libtool
libuchardet0 libxml2 m4 man-db mime-support po-debconf python python-all
python-atomicwrites python-attr python-avro python-certifi python-chardet
python-decorator python-docutils python-funcsigs python-h5py python-idna
python-iso8601 python-minimal python-more-itertools python-numpy
python-pathlib2 python-pbcommand python-pbcore python-pkg-resources
python-pluggy python-py python-pysam python-pytest python-requests
python-roman python-scandir python-scipy python-setuptools python-six
python-tz python-urllib3 python2 python2-minimal python2.7 python2.7-minimal
python3 python3-distutils python3-lib2to3 python3-minimal python3.7
python3.7-minimal sgml-base xml-core
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python-attr-doc
fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-funcsigs-doc
python-h5py-doc gfortran python-dev python-numpy-dbg python-numpy-doc
python-pbcore-doc subversion python-pytest-xdist python-mock
python-cryptography python-openssl python-socks python-scipy-doc
python-setuptools-doc python-ntlm python2-doc python2.7-doc binfmt-support
python3-doc python3-tk python3-venv python3.7-venv python3.7-doc
sgml-base-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl docutils-doc
libpaper-utils python-pil python-pygments python-dev python-cryptography
python-ipaddress python-openssl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file
gettext gettext-base groff-base intltool-debian libaec0 libarchive-zip-perl
libblas3 libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103
libhts2 libicu63 liblapack3 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libsz2 libtool
libuchardet0 libxml2 m4 man-db mime-support po-debconf python python-all
python-atomicwrites python-attr python-avro python-certifi python-chardet
python-decorator python-docutils python-funcsigs python-h5py python-idna
python-iso8601 python-minimal python-more-itertools python-numpy
python-pathlib2 python-pbcommand python-pbcore python-pkg-resources
python-pluggy python-py python-pysam python-pytest python-requests
python-roman python-scandir python-scipy python-setuptools python-six
python-tz python-urllib3 python2 python2-minimal python2.7 python2.7-minimal
python3 python3-distutils python3-lib2to3 python3-minimal python3.7
python3.7-minimal sbuild-build-depends-kineticstools-dummy sgml-base
xml-core
0 upgraded, 100 newly installed, 0 to remove and 0 not upgraded.
Need to get 54.6 MB of archives.
After this operation, 202 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HxdFYD/apt_archive ./ sbuild-build-depends-kineticstools-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-8 [394 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-8 [1089 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.6-1 [76.8 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-8 [1844 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-8 [299 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.7-minimal armhf 3.7.2-2 [582 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.7-minimal armhf 3.7.2-2 [1455 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.7.2-1 [36.6 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libpython3.7-stdlib armhf 3.7.2-2 [1662 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf python3.7 armhf 3.7.2-2 [323 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.7.2-1 [20.0 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.7.2-1 [61.5 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf sgml-base all 1.29 [14.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
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Get:51 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1 [1015 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.2-3 [76.7 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.2-3 [142 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180927 [95.8 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf xml-core all 0.18 [23.4 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf docutils-common all 0.14+dfsg-3 [204 kB]
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Get:70 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.15-4 [1044 B]
Get:72 http://172.17.0.1/private buster-staging/main armhf python-atomicwrites all 1.1.5-2 [6808 B]
Get:73 http://172.17.0.1/private buster-staging/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf python-avro all 1.8.2+dfsg-2 [59.4 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf python-certifi all 2018.8.24-1 [140 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.7.1-1 [181 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf python-chardet all 3.0.4-3 [80.6 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf python-decorator all 4.3.0-1.1 [14.4 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf python-roman all 2.0.0-3 [8688 B]
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Get:86 http://172.17.0.1/private buster-staging/main armhf python-more-itertools all 4.2.0-1 [42.3 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf python-scandir armhf 1.9.0-2 [17.1 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf python-pathlib2 all 2.3.3-1 [18.3 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf python-iso8601 all 0.1.11-1 [12.7 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf python-urllib3 all 1.24.1-1 [97.0 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf python-requests all 2.20.0-2 [66.8 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf python-tz all 2018.9-1 [33.5 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf python-pbcommand all 1.1.1-1 [88.7 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf python-pysam armhf 0.15.1+ds-1+rpi1 [1416 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf python-pbcore all 1.6.5+dfsg-1 [9100 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf python-pluggy all 0.8.0-1 [20.5 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf python-py all 1.7.0-2 [86.5 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf python-pytest all 3.10.1-2 [243 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf python-scipy armhf 1.1.0-2 [8980 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 40.7.1-1 [381 kB]
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Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libblas3:armhf (3.8.0-2) ...
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
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libpython2-stdlib:armhf (2.7.15-4) ...
Setting up libhts2:armhf (1.9-8) ...
Setting up libtool (2.4.6-9) ...
Setting up libpython3-stdlib:armhf (3.7.2-1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3 (3.7.2-1) ...
Setting up liblapack3:armhf (3.8.0-2) ...
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 python2 (2.7.15-4) ...
Setting up libpython-stdlib:armhf (2.7.15-4) ...
Setting up python3-lib2to3 (3.7.2-3) ...
Setting up python3-distutils (3.7.2-3) ...
Setting up python (2.7.15-4) ...
Setting up python-idna (2.6-1) ...
Setting up python-atomicwrites (1.1.5-2) ...
Setting up python-attr (18.2.0-1) ...
Setting up python-scandir (1.9.0-2) ...
Setting up python-pysam (0.15.1+ds-1+rpi1) ...
Setting up python-pluggy (0.8.0-1) ...
Setting up python-certifi (2018.8.24-1) ...
Setting up python-tz (2018.9-1) ...
Setting up python-avro (1.8.2+dfsg-2) ...
Setting up python-pkg-resources (40.7.1-1) ...
Setting up python-roman (2.0.0-3) ...
Setting up python-numpy (1:1.16.1-1) ...
Setting up python-six (1.12.0-1) ...
Setting up python-pbcore (1.6.5+dfsg-1) ...
Setting up python-funcsigs (1.0.2-4) ...
Setting up python-iso8601 (0.1.11-1) ...
Setting up python-decorator (4.3.0-1.1) ...
Setting up python-pathlib2 (2.3.3-1) ...
Setting up dh-python (3.20180927) ...
Setting up python-all (2.7.15-4) ...
Setting up python-setuptools (40.7.1-1) ...
Setting up python-urllib3 (1.24.1-1) ...
Setting up python-h5py (2.8.0-3) ...
Setting up python-chardet (3.0.4-3) ...
Setting up python-scipy (1.1.0-2) ...
Setting up python-py (1.7.0-2) ...
Setting up python-more-itertools (4.2.0-1) ...
Setting up python-pytest (3.10.1-2) ...
Setting up python-requests (2.20.0-2) ...
Setting up python-pbcommand (1.1.1-1) ...
Processing triggers for sgml-base (1.29) ...
Setting up docutils-common (0.14+dfsg-3) ...
Processing triggers for sgml-base (1.29) ...
Setting up python-docutils (0.14+dfsg-3) ...
update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.1) ...
Setting up sbuild-build-depends-kineticstools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-20+rpi1 gcc-8_8.2.0-20+rpi1 libc6-dev_2.28-6+rpi1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-20+rpi1 dash_0.5.10.2-5 debconf_1.5.70 debhelper_12.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-python_3.20180927 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 docutils-common_0.14+dfsg-3 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-20+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-20+rpi1 gcc-8-base_8.2.0-20+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-3 libaec0_1.0.2-1 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-20+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-20+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-6+rpi1 libc-dev-bin_2.28-6+rpi1 libc6_2.28-6+rpi1 libc6-dev_2.28-6+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.2.0-20+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.2 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.2.0-20+rpi1 libgcc1_1:8.2.0-20+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-20+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-20+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libhdf5-103_1.10.4+repack-10 libhogweed4_3.4.1-1 libhts2_1.9-8 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libpython3-stdlib_3.7.2-1 libpython3.7-minimal_3.7.2-2 libpython3.7-stdlib_3.7.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 libsystemd0_240-5+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.2.0-20+rpi1 libuchardet0_0.0.6-3 libudev1_240-5+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 multiarch-support_2.28-6+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-all_2.7.15-4 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-avro_1.8.2+dfsg-2 python-certifi_2018.8.24-1 python-chardet_3.0.4-3 python-decorator_4.3.0-1.1 python-docutils_0.14+dfsg-3 python-funcsigs_1.0.2-4 python-h5py_2.8.0-3 python-idna_2.6-1 python-iso8601_0.1.11-1 python-minimal_2.7.15-4 python-more-itertools_4.2.0-1 python-numpy_1:1.16.1-1 python-pathlib2_2.3.3-1 python-pbcommand_1.1.1-1 python-pbcore_1.6.5+dfsg-1 python-pkg-resources_40.7.1-1 python-pluggy_0.8.0-1 python-py_1.7.0-2 python-pysam_0.15.1+ds-1+rpi1 python-pytest_3.10.1-2 python-requests_2.20.0-2 python-roman_2.0.0-3 python-scandir_1.9.0-2 python-scipy_1.1.0-2 python-setuptools_40.7.1-1 python-six_1.12.0-1 python-tz_2018.9-1 python-urllib3_1.24.1-1 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 python3_3.7.2-1 python3-distutils_3.7.2-3 python3-lib2to3_3.7.2-3 python3-minimal_3.7.2-1 python3.7_3.7.2-2 python3.7-minimal_3.7.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kineticstools-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sgml-base_1.29 systemd_240-5+rpi1 sysvinit-utils_2.93-6 tar_1.30+dfsg-5 tzdata_2018i-1 udev_240-5+rpi1 util-linux_2.33.1-0.1 xml-core_0.18 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 14 12:44:42 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./kineticstools_0.6.1+git20180425.27a1878-2.dsc
dpkg-source: info: extracting kineticstools in /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878
dpkg-source: info: unpacking kineticstools_0.6.1+git20180425.27a1878.orig.tar.xz
dpkg-source: info: unpacking kineticstools_0.6.1+git20180425.27a1878-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying man-pages.patch
dpkg-source: info: applying tests-import.patch
dpkg-source: info: applying verbose-testing.patch
dpkg-source: info: applying deactivate-tests-requiring-unavailable-data.patch
dpkg-source: info: applying compiled-extension.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying ignore_h5py_deprecation_warnings_in_test.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c5ffed34-aab0-4849-9090-9004f5515dda
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package kineticstools
dpkg-buildpackage: info: source version 0.6.1+git20180425.27a1878-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2 --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:217: python2.7 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py build
running build
running build_py
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
copying kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal
copying kineticsTools/internal/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal
copying kineticsTools/internal/basic.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks
copying kineticsTools/tasks/gather_kinetics_h5.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/SP2-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
copying kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources
running build_ext
building 'kineticsTools/tree_predict' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/kineticsTools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c kineticsTools/tree_predict.c -o build/temp.linux-armhf-2.7/kineticsTools/tree_predict.o -O3 -shared -std=c99
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-4bazB0/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/kineticsTools/tree_predict.o -o /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tree_predict.so
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:217: cd /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build; python2.7 -m pytest test
============================= test session starts ==============================
platform linux2 -- Python 2.7.15+, pytest-3.10.1, py-1.7.0, pluggy-0.8.0
rootdir: /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878, inifile:
collected 29 items
test/test_ReferenceUtils.py ssssss [ 20%]
test/test_gather_h5.py ... [ 31%]
test/test_inputs.py ssssssssss [ 65%]
test/test_internal.py .... [ 79%]
test/test_outputs.py sss [ 89%]
test/test_tool_contract.py sss [100%]
=============================== warnings summary ===============================
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:75
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:75: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
"ZZZZZZZ", dtype=np.uint8).reshape(7, 7)
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:83
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:83: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
"ZZZZZZZ", dtype=np.uint8).reshape(7, 7)
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:91
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:91: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
"ZZZZZZZ", dtype=np.uint8).reshape(7, 7)
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:99
/usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py:99: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
"ZZZZZZZ", dtype=np.uint8).reshape(7, 7)
-- Docs: https://docs.pytest.org/en/latest/warnings.html
============== 7 passed, 22 skipped, 4 warnings in 19.32 seconds ===============
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python2 --buildsystem=pybuild
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878'
dh_auto_install
I: pybuild base:217: /usr/bin/python setup.py install --root /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools
running install
running build
running build_py
running build_ext
running install_lib
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/basic.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/internal/basic.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/gather_kinetics_h5.py -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tasks/gather_kinetics_h5.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
creating /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/SP2-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/tree_predict.so -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ReferenceUtils.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ResultWriter.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/pipelineTools.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/KineticWorker.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MixtureEstimationMethods.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteCommon.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MultiSiteDetection.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/MedakaLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/BasicLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/PositiveControlEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ModificationDecode.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/WorkerProcess.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/ipdModel.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/.pybuild/cpython2_2.7_kineticstools/build/kineticsTools/sharedArray.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py to sharedArray.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py to ipdModel.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/internal/basic.py to basic.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py to gather_kinetics_h5.pyc
running install_egg_info
running egg_info
creating kineticsTools.egg-info
writing requirements to kineticsTools.egg-info/requires.txt
writing kineticsTools.egg-info/PKG-INFO
writing top-level names to kineticsTools.egg-info/top_level.txt
writing dependency_links to kineticsTools.egg-info/dependency_links.txt
writing entry points to kineticsTools.egg-info/entry_points.txt
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest file 'kineticsTools.egg-info/SOURCES.txt'
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
Copying kineticsTools.egg-info to /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ipdSummary script to /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/bin
Installing summarizeModifications script to /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/python-kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/bin
mv debian/python-kineticstools/usr/bin/* /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/share/man//man1
rst2man doc/manual.rst > /<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878/debian/kineticstools/usr/share/man//man1/ipdSummary.1
doc/manual.rst:117: (ERROR/3) Malformed table.
Text in column margin in table line 2.
================ ===========
Column Description
================ ===========
seqid Fasta contig name
source Name of tool -- 'kinModCall'
type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature
start Modification position on contig
end Modification position on contig
score Phred transformed p-value of detection - this is the single-site detection p-value
strand Sample strand containing modification
phase Not applicable
attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes.
================ ===========
doc/manual.rst:46: (WARNING/2) "math" role not supported
doc/manual.rst:48: (WARNING/2) "math" role not supported
doc/manual.rst:48: (WARNING/2) "math" role not supported
mkdir -p debian/kineticstools-data/usr/share/kineticstools
mv debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/
make[1]: Leaving directory '/<<BUILDDIR>>/kineticstools-0.6.1+git20180425.27a1878'
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_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:329: renaming tree_predict.so to tree_predict.arm-linux-gnueabihf.so
dh_installinit -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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.arm-linux-gnueabihf.so was not linked against libpthread.so.0 (it uses none of the library's symbols)
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Provides} unused, but is defined
dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Versions} unused, but is defined
dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Provides} unused, but is defined
dpkg-gencontrol: warning: package python-kineticstools: substitution variable ${python:Versions} unused, but is defined
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-kineticstools' in '../python-kineticstools_0.6.1+git20180425.27a1878-2_armhf.deb'.
dpkg-deb: building package 'python-kineticstools-dbgsym' in '../python-kineticstools-dbgsym_0.6.1+git20180425.27a1878-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kineticstools_0.6.1+git20180425.27a1878-2_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 2019-02-24T05:00:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kineticstools_0.6.1+git20180425.27a1878-2_armhf.changes:
--------------------------------------------------------
Format: 1.8
Date: Thu, 14 Feb 2019 13:36:28 +0100
Source: kineticstools
Binary: kineticstools kineticstools-data python-kineticstools
Architecture: armhf
Version: 0.6.1+git20180425.27a1878-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
kineticstools - detection of DNA modifications
kineticstools-data - detection of DNA modifications -- data files
python-kineticstools - detection of DNA modifications (Python 2 library)
Closes: 921382
Changes:
kineticstools (0.6.1+git20180425.27a1878-2) unstable; urgency=medium
.
* Ignore deprecation warnings breaking test suite
Closes: #921382
* Add myself to Uploaders since Afif has removed himself (Thanks for your
work on this package, Afif)
Checksums-Sha1:
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Checksums-Sha256:
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6e972d0141ab5ed036b93aa68f27d8a4698a0891a6d1a226f75c1f9483d246b8 6220 python-kineticstools-dbgsym_0.6.1+git20180425.27a1878-2_armhf.deb
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Files:
413a5b8f388191c84d6ac0726fae4d79 7378 science optional kineticstools_0.6.1+git20180425.27a1878-2_armhf.buildinfo
f1a89fb49396eda0f2410042ce39e007 6220 debug optional python-kineticstools-dbgsym_0.6.1+git20180425.27a1878-2_armhf.deb
e2f0f28bca83e86dbafb714037ad2862 49188 python optional python-kineticstools_0.6.1+git20180425.27a1878-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python-kineticstools-dbgsym_0.6.1+git20180425.27a1878-2_armhf.deb
-----------------------------------------------------------------
new Debian package, version 2.0.
size 6220 bytes: control archive=564 bytes.
454 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: python-kineticstools-dbgsym
Source: kineticstools
Version: 0.6.1+git20180425.27a1878-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18
Depends: python-kineticstools (= 0.6.1+git20180425.27a1878-2)
Section: debug
Priority: optional
Description: debug symbols for python-kineticstools
Build-Ids: 3cf6a9480737d160da26ea051f490aa888a2ba82
drwxr-xr-x root/root 0 2019-02-14 12:36 ./
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/debug/.build-id/3c/
-rw-r--r-- root/root 7836 2019-02-14 12:36 ./usr/lib/debug/.build-id/3c/f6a9480737d160da26ea051f490aa888a2ba82.debug
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/share/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-14 12:36 ./usr/share/doc/python-kineticstools-dbgsym -> python-kineticstools
python-kineticstools_0.6.1+git20180425.27a1878-2_armhf.deb
----------------------------------------------------------
new Debian package, version 2.0.
size 49188 bytes: control archive=2044 bytes.
1120 bytes, 21 lines control
3111 bytes, 31 lines md5sums
170 bytes, 9 lines * postinst #!/bin/sh
279 bytes, 14 lines * prerm #!/bin/sh
Package: python-kineticstools
Source: kineticstools
Version: 0.6.1+git20180425.27a1878-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 264
Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcommand, python-pbcore, python-scipy, python:any (<< 2.8), python:any (>= 2.7~), kineticstools-data (= 0.6.1+git20180425.27a1878-2)
Suggests: python-pybigwig
Section: python
Priority: optional
Homepage: https://github.com/PacificBiosciences/kineticsTools
Description: detection of DNA modifications (Python 2 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 2 library.
drwxr-xr-x root/root 0 2019-02-14 12:36 ./
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/
-rw-r--r-- root/root 1831 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/dependency_links.txt
-rw-r--r-- root/root 129 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/entry_points.txt
-rw-r--r-- root/root 1 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/not-zip-safe
-rw-r--r-- root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/requires.txt
-rw-r--r-- root/root 41 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/top_level.txt
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools/
-rw-r--r-- root/root 2679 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py
-rw-r--r-- root/root 35903 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py
-rw-r--r-- root/root 3686 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py
-rw-r--r-- root/root 12621 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py
-rw-r--r-- root/root 15734 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py
-rw-r--r-- root/root 6915 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py
-rw-r--r-- root/root 11427 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py
-rw-r--r-- root/root 4959 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py
-rw-r--r-- root/root 6571 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py
-rw-r--r-- root/root 38134 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py
-rw-r--r-- root/root 9249 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py
-rw-r--r-- root/root 1829 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/__init__.py
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools/internal/
-rw-r--r-- root/root 140 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/internal/__init__.py
-rw-r--r-- root/root 1979 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/internal/basic.py
-rw-r--r-- root/root 22765 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py
-rw-r--r-- root/root 30780 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py
-rw-r--r-- root/root 2181 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py
lrwxrwxrwx root/root 0 2019-02-14 12:36 ./usr/lib/python2.7/dist-packages/kineticsTools/resources -> ../../../../share/kineticstools/resources
-rw-r--r-- root/root 2399 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py
-rw-r--r-- root/root 7924 2018-04-25 19:28 ./usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py
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drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/share/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-02-14 12:36 ./usr/share/doc/python-kineticstools/
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-rw-r--r-- root/root 2037 2019-02-14 12:36 ./usr/share/doc/python-kineticstools/copyright
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| Summary |
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Build Architecture: armhf
Build-Space: 352204
Build-Time: 83
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 785
Job: kineticstools_0.6.1+git20180425.27a1878-2
Machine Architecture: armhf
Package: kineticstools
Package-Time: 952
Source-Version: 0.6.1+git20180425.27a1878-2
Space: 352204
Status: successful
Version: 0.6.1+git20180425.27a1878-2
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Finished at 2019-02-24T05:00:56Z
Build needed 00:15:52, 352204k disc space