kineticstools →
0.5.2+dfsg-1 →
armhf → 2016-07-08 11:52:33
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-03
+==============================================================================+
| kineticstools 0.5.2+dfsg-1 (armhf) 08 Jul 2016 11:29 |
+==============================================================================+
Package: kineticstools
Version: 0.5.2+dfsg-1
Source Version: 0.5.2+dfsg-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/kineticstools-IdaGsY/kineticstools-0.5.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kineticstools-IdaGsY' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-f0a22688-1b58-4d80-8e9b-ac4ecc21a2cf' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9128 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.1 MB]
Fetched 20.2 MB in 22s (888 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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://anonscm.debian.org/git/debian-med/kineticstools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/kineticstools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 114 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main kineticstools 0.5.2+dfsg-1 (dsc) [2399 B]
Get:2 http://172.17.0.1/private stretch-staging/main kineticstools 0.5.2+dfsg-1 (tar) [114 MB]
Get:3 http://172.17.0.1/private stretch-staging/main kineticstools 0.5.2+dfsg-1 (diff) [5872 B]
Fetched 114 MB in 14s (7660 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-824j1B/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-824j1B/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 52 not upgraded.
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After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-824j1B/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 13868 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose
Filtered Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose
dpkg-deb: building package 'sbuild-build-depends-kineticstools-dummy' in '/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive/sbuild-build-depends-kineticstools-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Sources [292 B]
Get:5 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ Packages [611 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install kineticstools build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
file gettext gettext-base groff-base intltool-debian libaec0
libarchive-zip-perl libblas-common libblas3 libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhdf5-10
libhogweed4 libhts1 libicu55 libidn11 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 libldap-2.4-2 libmagic1 libmpdec2 libnettle6
libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libsqlite3-0 libssh2-1 libssl1.0.2 libsz2 libtasn1-6 libtimedate-perl
libtool libunistring0 libxml2 m4 man-db mime-support openssl po-debconf
python python-all python-avro python-chardet python-decorator
python-docutils python-funcsigs python-functools32 python-h5py
python-iso8601 python-jsonschema python-minimal python-mock python-nose
python-numpy python-pbcommand python-pbcore python-pbr python-pkg-resources
python-pysam python-requests python-roman python-scipy python-setuptools
python-six python-urllib3 python-xmlbuilder python2.7 python2.7-minimal
python3 python3-minimal python3.5 python3.5-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
gnutls-bin krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler
gcj-jdk less www-browser libmail-box-perl python-doc python-tk
texlive-latex-recommended texlive-latex-base texlive-lang-french
fonts-linuxlibertine | ttf-linux-libertine python-funcsigs-doc
python-mock-doc python-coverage python-nose-doc gfortran python-dev
python-numpy-dbg python-numpy-doc python-pbcore-doc python-ndg-httpsclient
python-openssl python-pyasn1 python-socks python-scipy-doc
python-setuptools-doc python-ntlm python-xmlbuilder-doc python2.7-doc
binfmt-support python3-doc python3-tk python3-venv python3.5-venv
python3.5-doc sgml-base-doc
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
krb5-locales libsasl2-modules libltdl-dev libmail-sendmail-perl python-pil
python-pygments libpaper-utils docutils-doc python-dev python-imaging
python-ndg-httpsclient python-openssl python-pyasn1
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
file gettext gettext-base groff-base intltool-debian libaec0
libarchive-zip-perl libblas-common libblas3 libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhdf5-10
libhogweed4 libhts1 libicu55 libidn11 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 libldap-2.4-2 libmagic1 libmpdec2 libnettle6
libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
libsqlite3-0 libssh2-1 libssl1.0.2 libsz2 libtasn1-6 libtimedate-perl
libtool libunistring0 libxml2 m4 man-db mime-support openssl po-debconf
python python-all python-avro python-chardet python-decorator
python-docutils python-funcsigs python-functools32 python-h5py
python-iso8601 python-jsonschema python-minimal python-mock python-nose
python-numpy python-pbcommand python-pbcore python-pbr python-pkg-resources
python-pysam python-requests python-roman python-scipy python-setuptools
python-six python-urllib3 python-xmlbuilder python2.7 python2.7-minimal
python3 python3-minimal python3.5 python3.5-minimal
sbuild-build-depends-kineticstools-dummy sgml-base xml-core
0 upgraded, 107 newly installed, 0 to remove and 52 not upgraded.
Need to get 45.4 MB/56.6 MB of archives.
After this operation, 198 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-Hqd5NZ/apt_archive ./ sbuild-build-depends-kineticstools-dummy 0.invalid.0 [848 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.12-1 [387 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-1 [1167 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.13.0-1 [479 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-1 [1844 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-1 [276 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python-xmlbuilder all 1.0-1 [5884 B]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.2-1 [562 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.2-1 [1423 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-4 [35.3 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.2-1 [2081 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.2-1 [210 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-4 [18.6 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20160609 [78.4 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-4 [21.7 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf sgml-base all 1.28 [14.7 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-2 [269 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-2 [62.4 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3.1 [110 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.8-1 [44.1 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.13-1 [737 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.2+dfsg-1 [57.2 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.2+dfsg-1 [111 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.2+dfsg-1 [261 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.2+dfsg-1 [131 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [65.6 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [96.7 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2h-1 [667 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.019-1 [12.2 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.019-1 [7352 B]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf docutils-common all 0.12+dfsg-1 [185 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-1 [13.8 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-1+rpi1 [166 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-1 [112 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.11.1-1 [66.6 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.5.0-2.1 [121 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.47.0-1 [244 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8 [981 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-1+rpi1 [215 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-1 [1395 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf python-all armhf 2.7.11-2 [940 B]
Get:77 http://172.17.0.1/private stretch-staging/main armhf python-avro all 1.8.0+dfsg-2 [57.1 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf python-pkg-resources all 20.10.1-1.1 [141 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf python-chardet all 2.3.0-2 [96.0 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf python-decorator all 4.0.6-1 [12.7 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf python-roman all 2.0.0-2 [8130 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf python-docutils all 0.12+dfsg-1 [361 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf python-funcsigs all 0.4-2 [12.8 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf python-functools32 all 3.2.3.2-2 [10.8 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf python-numpy armhf 1:1.11.1~rc1-1 [1599 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf python-six all 1.10.0-3 [14.4 kB]
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Get:88 http://172.17.0.1/private stretch-staging/main armhf python-pbr all 1.8.0-4.1 [47.2 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf python-mock all 1.3.0-2.1 [58.2 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf python-jsonschema all 2.5.1-5 [32.6 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf python-nose all 1.3.7-2 [132 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf python-iso8601 all 0.1.11-1 [12.7 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf python-urllib3 all 1.15.1-2 [70.1 kB]
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Get:95 http://172.17.0.1/private stretch-staging/main armhf python-pbcommand all 0.3.22-2 [63.9 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf python-pysam armhf 0.9.0+ds-1 [937 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf python-pbcore all 1.2.9+dfsg-1 [9080 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf python-setuptools all 20.10.1-1.1 [203 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf python-scipy armhf 0.17.1-1 [7842 kB]
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Setting up python3.5 (3.5.2-1) ...
Setting up libpython3-stdlib:armhf (3.5.1-4) ...
Setting up sgml-base (1.28) ...
Setting up libmagic1:armhf (1:5.28-2) ...
Setting up file (1:5.28-2) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libnettle6:armhf (3.2-1) ...
Setting up libhogweed4:armhf (3.2-1) ...
Setting up libidn11:armhf (1.32-3.1) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up libtasn1-6:armhf (4.8-1) ...
Setting up libgnutls30:armhf (3.4.13-1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up libkrb5support0:armhf (1.14.2+dfsg-1) ...
Setting up libk5crypto3:armhf (1.14.2+dfsg-1) ...
Setting up libkrb5-3:armhf (1.14.2+dfsg-1) ...
Setting up libgssapi-krb5-2:armhf (1.14.2+dfsg-1) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-15) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-15) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1.2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20160430.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.8.1-1) ...
Setting up openssl (1.0.2h-1) ...
Setting up ca-certificates (20160104) ...
Setting up libglib2.0-0:armhf (2.48.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.019-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up xml-core (0.13+nmu2) ...
Setting up docutils-common (0.12+dfsg-1) ...
Setting up libaec0:armhf (0.3.2-1) ...
Setting up libblas-common (3.6.1-1) ...
Setting up libgfortran3:armhf (6.1.1-1+rpi1) ...
Setting up libblas3 (3.6.1-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libnghttp2-14:armhf (1.11.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up libssh2-1:armhf (1.5.0-2.1) ...
Setting up libcurl3-gnutls:armhf (7.47.0-1) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up libhdf5-10:armhf (1.8.16+docs-8) ...
Setting up libhts1:armhf (1.3.1-1+rpi1) ...
Setting up liblapack3 (3.6.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up python-all (2.7.11-2) ...
Setting up python-avro (1.8.0+dfsg-2) ...
Setting up python-pkg-resources (20.10.1-1.1) ...
Setting up python-chardet (2.3.0-2) ...
Setting up python-decorator (4.0.6-1) ...
Setting up python-roman (2.0.0-2) ...
Setting up python-funcsigs (0.4-2) ...
Setting up python-functools32 (3.2.3.2-2) ...
Setting up python-numpy (1:1.11.1~rc1-1) ...
Setting up python-six (1.10.0-3) ...
Setting up python-h5py (2.6.0-1) ...
Setting up python-pbr (1.8.0-4.1) ...
update-alternatives: using /usr/bin/python2-pbr to provide /usr/bin/pbr (pbr) in auto mode
Setting up python-mock (1.3.0-2.1) ...
Setting up python-jsonschema (2.5.1-5) ...
update-alternatives: using /usr/bin/python2-jsonschema to provide /usr/bin/jsonschema (jsonschema) in auto mode
Setting up python-nose (1.3.7-2) ...
Setting up python-iso8601 (0.1.11-1) ...
Setting up python-urllib3 (1.15.1-2) ...
Setting up python-requests (2.10.0-2) ...
Setting up python-pbcommand (0.3.22-2) ...
Setting up python-pysam (0.9.0+ds-1) ...
Setting up python-pbcore (1.2.9+dfsg-1) ...
Setting up python-setuptools (20.10.1-1.1) ...
Setting up python-scipy (0.17.1-1) ...
Processing triggers for sgml-base (1.28) ...
Setting up python-docutils (0.12+dfsg-1) ...
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/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-python (2.20160609) ...
Setting up python3 (3.5.1-4) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-kineticstools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.019-1) ...
Processing triggers for libc-bin (2.22-9) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-10 dpkg-dev_1.18.7 g++-5_5.3.1-21 gcc-5_5.3.1-21 libc6-dev_2.22-9 libstdc++-5-dev_5.3.1-21 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.12 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-10 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 console-setup_1.146 console-setup-linux_1.146 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-3 cpp-5_5.3.1-21 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-python_2.20160609 dh-strip-nondeterminism_0.019-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1 docutils-common_0.12+dfsg-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43-3 e2fsprogs_1.43-3 fakeroot_1.20.2-2 file_1:5.28-2 findutils_4.6.0+git+20160126-2 fuse2fs_1.43-3 g++_4:5.3.1-3 g++-5_5.3.1-21 gcc_4:5.3.1-3 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_4.9.3-14 gcc-5_5.3.1-21 gcc-5-base_5.3.1-21 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-3 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 ifupdown_0.8.13 init_1.34 init-system-helpers_1.34 initscripts_2.88dsf-59.4 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 iproute2_4.3.0-1 kbd_2.0.3-2 keyboard-configuration_1.146 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec0_0.3.2-1 libapparmor1_2.10-4 libapt-pkg5.0_1.2.12 libarchive-zip-perl_1.57-1 libasan2_5.3.1-21 libatm1_1:2.5.1-1.5 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libblas-common_3.6.1-1 libblas3_3.6.1-1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-9 libc-dev-bin_2.22-9 libc6_2.22-9 libc6-dev_2.22-9 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43-3 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcurl3-gnutls_7.47.0-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.213 libdevmapper1.02.1_2:1.02.124-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.2.0-1 libfakeroot_1.20.2-2 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.019-1 libfuse2_2.9.6-1 libgc1c2_1:7.4.2-8 libgcc-5-dev_5.3.1-21 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libgfortran3_6.1.1-1+rpi1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.13-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.22-2 libgssapi-krb5-2_1.14.2+dfsg-1 libhdf5-10_1.8.16+docs-8 libhogweed4_3.2-1 libhts1_1.3.1-1+rpi1 libicu55_55.1-7 libidn11_1.32-3.1 libisl15_0.17.1-1 libk5crypto3_1.14.2+dfsg-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.2+dfsg-1 libkrb5support0_1.14.2+dfsg-1 liblapack3_3.6.1-1 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblocale-gettext-perl_1.07-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.28-2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160319-1 libncursesw5_6.0+20160319-1 libnettle6_3.2-1 libnghttp2-14_1.11.1-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-1 libpython2.7-stdlib_2.7.12-1 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.2-1 libpython3.5-stdlib_3.5.2-1 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libsqlite3-0_3.13.0-1 libss2_1.43-3 libssh2-1_1.5.0-2.1 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.3.1-21 libstdc++6_6.1.1-1+rpi1 libsystemd0_230-2 libsz2_0.3.2-1 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_230-2 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libxml2_2.9.3+dfsg1-1.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.22-9 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 netbase_5.3 openssl_1.0.2h-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 po-debconf_1.0.19 procps_2:3.3.11-3 psmisc_22.21-2.1 python_2.7.11-2 python-all_2.7.11-2 python-avro_1.8.0+dfsg-2 python-chardet_2.3.0-2 python-decorator_4.0.6-1 python-docutils_0.12+dfsg-1 python-funcsigs_0.4-2 python-functools32_3.2.3.2-2 python-h5py_2.6.0-1 python-iso8601_0.1.11-1 python-jsonschema_2.5.1-5 python-minimal_2.7.11-2 python-mock_1.3.0-2.1 python-nose_1.3.7-2 python-numpy_1:1.11.1~rc1-1 python-pbcommand_0.3.22-2 python-pbcore_1.2.9+dfsg-1 python-pbr_1.8.0-4.1 python-pkg-resources_20.10.1-1.1 python-pysam_0.9.0+ds-1 python-requests_2.10.0-2 python-roman_2.0.0-2 python-scipy_0.17.1-1 python-setuptools_20.10.1-1.1 python-six_1.10.0-3 python-urllib3_1.15.1-2 python-xmlbuilder_1.0-1 python2.7_2.7.12-1 python2.7-minimal_2.7.12-1 python3_3.5.1-4 python3-minimal_3.5.1-4 python3.5_3.5.2-1 python3.5-minimal_3.5.2-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kineticstools-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 sgml-base_1.28 startpar_0.59-3 systemd_230-2 systemd-sysv_230-2 sysv-rc_2.88dsf-59.4 sysvinit-utils_2.88dsf-59.4 tar_1.29-1+rpi1 tzdata_2016d-2 udev_230-2 util-linux_2.28-5 xkb-data_2.17-1 xml-core_0.13+nmu2 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Jul 3 03:09:18 2016 UTC using RSA key ID 3AF9DDC1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./kineticstools_0.5.2+dfsg-1.dsc
dpkg-source: info: extracting kineticstools in kineticstools-0.5.2+dfsg
dpkg-source: info: unpacking kineticstools_0.5.2+dfsg.orig.tar.gz
dpkg-source: info: unpacking kineticstools_0.5.2+dfsg-1.debian.tar.xz
dpkg-source: info: applying man-pages.patch
dpkg-source: info: applying tests-import.patch
dpkg-source: info: applying deactivate-tests-requiring-unavailable-data.patch
dpkg-source: info: applying verbose-testing.patch
dpkg-source: info: applying compiled-extension.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-f0a22688-1b58-4d80-8e9b-ac4ecc21a2cf
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 0.5.2+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build kineticstools-0.5.2+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2 --buildsystem=pybuild
dh_testdir -a -O--buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build
running build
running build_py
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin
copying ./bin/__init__.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin
copying ./bin/copyIpdSummaryDataset.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin
copying ./bin/writeSummaryToCmp.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin
copying ./bin/testShared.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying ./kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying ./kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
running build_ext
building 'kineticsTools/tree_predict' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/kineticsTools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -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-armv7l-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 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/kineticsTools/tree_predict.o -o /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:184: cd /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose test
Check the null model against a few hard-coded contexts ... ok
Test a modification decode around a known modification in lambda ... ok
runTest (test.TestSetup) ... ok
test_bam (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_cmph5 (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_createReferenceWindows (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_dataset (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_enumerateChunks (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_parseReferenceWindow (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_private_api (test_inputs.TestBam) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_small_decode (test_inputs.TestChunkedDataset) ... SKIP: Missing test data directory
test_private_api (test_inputs.TestDataset) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_small_decode (test_inputs.TestNonStochastic) ... SKIP: Missing test data directory
test_private_api (test_inputs.TestSplitDataset) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_run_e2e (test_tool_contract.TestIpdSummary) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestIpdSummaryChunk) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestSummarizeModifications) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
----------------------------------------------------------------------
Ran 20 tests in 625.898s
OK (SKIP=17)
Pos: 3, TplStrand: 0
Got ctx: NGGGCGGCGACCTCG
Lut prediction: 0.692615
Gbm prediction: 0.692615
Gbm prediction fast: 0.692615
Gbm pred via predictIpdFuncModel: 0.692615
Methylated prediction: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction: NGGGCGGCGJCCTCG -> 0.481690
Methylated prediction fast: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction fast: NGGGCGGCGJCCTCG -> 0.481690
Pos: 10, TplStrand: 0
Got ctx: CGACCTCGCGGGTTT
Lut prediction: 0.439837
Gbm prediction: 0.439837
Gbm prediction fast: 0.439837
Gbm pred via predictIpdFuncModel: 0.439837
Methylated prediction: CGACJTCGCGGGTTT -> 1.806269
Methylated prediction: CGACCTCGCJGGTTT -> 0.418073
Methylated prediction fast: CGACJTCGCGGGTTT -> 1.806269
Methylated prediction fast: CGACCTCGCJGGTTT -> 0.418073
Pos: 20, TplStrand: 0
Got ctx: GGTTTTCGCTATTTA
Lut prediction: 0.803713
Gbm prediction: 0.803713
Gbm prediction fast: 0.803713
Gbm pred via predictIpdFuncModel: 0.803713
Pos: 30, TplStrand: 0
Got ctx: ATTTATGAAAATTTT
Lut prediction: 0.497546
Gbm prediction: 0.497546
Gbm prediction fast: 0.497546
Gbm pred via predictIpdFuncModel: 0.497546
Methylated prediction: ATTTHTGAAAATTTT -> 3.467282
Methylated prediction: ATTTATGAAHATTTT -> 0.462962
Methylated prediction fast: ATTTHTGAAAATTTT -> 3.467282
Methylated prediction fast: ATTTATGAAHATTTT -> 0.462962
Pos: 31, TplStrand: 0
Got ctx: TTTATGAAAATTTTC
Lut prediction: 0.425639
Gbm prediction: 0.425639
Gbm prediction fast: 0.425639
Gbm pred via predictIpdFuncModel: 0.425639
Pos: 32, TplStrand: 0
Got ctx: TTATGAAAATTTTCC
Lut prediction: 0.387926
Gbm prediction: 0.387926
Gbm prediction fast: 0.387926
Gbm pred via predictIpdFuncModel: 0.387926
Pos: 33, TplStrand: 0
Got ctx: TATGAAAATTTTCCG
Lut prediction: 1.008767
Gbm prediction: 1.008767
Gbm prediction fast: 1.008767
Gbm pred via predictIpdFuncModel: 1.008767
Methylated prediction: TATGHAAATTTTCCG -> 6.857647
Methylated prediction: TATGAAAATHTTCCG -> 1.047730
Methylated prediction fast: TATGHAAATTTTCCG -> 6.857647
Methylated prediction fast: TATGAAAATHTTCCG -> 1.047730
Pos: 34, TplStrand: 0
Got ctx: ATGAAAATTTTCCGG
Lut prediction: 1.700875
Gbm prediction: 1.700875
Gbm prediction fast: 1.700875
Gbm pred via predictIpdFuncModel: 1.700875
Methylated prediction: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction: ATGAAAATTHTCCGG -> 2.211950
Methylated prediction fast: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction fast: ATGAAAATTHTCCGG -> 2.211950
[{'LLR': 44.9363980691445, 'tpl': 14982, 'Mask': [-5, 0], 'modification': 'm6A', 'strand': 0, 'QMod': 195.15629718037397}, {'LLR': 0.7833812384793148, 'tpl': 15040, 'Mask': [-1, 3], 'modification': 'm6A', 'strand': 1, 'QMod': 5.0363556562304366}, {'LLR': 45.588426682175815, 'tpl': 14991, 'Mask': [-5, 0, 1], 'modification': 'm6A', 'strand': 1, 'QMod': 197.98802146719927}, {'LLR': 12.04025630132049, 'tpl': 14997, 'Mask': [-8, -5, 1, 2, 3], 'modification': 'm4C', 'strand': 1, 'QMod': 52.290194354679265}, {'LLR': 5.787841909938088, 'tpl': 14996, 'Mask': [-6, -3, 1, 2], 'modification': 'm4C', 'strand': 1, 'QMod': 25.14956702352173}]
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-0.5.2+dfsg'
dh_auto_install
I: pybuild base:184: /usr/bin/python setup.py install --root /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools
running install
running build
running build_py
running build_ext
running install_lib
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin/__init__.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin/copyIpdSummaryDataset.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin/writeSummaryToCmp.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/bin/testShared.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.pyc -> /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin/copyIpdSummaryDataset.py to copyIpdSummaryDataset.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin/writeSummaryToCmp.py to writeSummaryToCmp.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/bin/testShared.py to testShared.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py to ModificationDecode.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py to MultiSiteCommon.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py to pipelineTools.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py to sharedArray.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py to ipdModel.pyc
running install_egg_info
running egg_info
creating kineticsTools.egg-info
writing requirements to kineticsTools.egg-info/requires.txt
writing kineticsTools.egg-info/PKG-INFO
writing top-level names to kineticsTools.egg-info/top_level.txt
writing dependency_links to kineticsTools.egg-info/dependency_links.txt
writing entry points to kineticsTools.egg-info/entry_points.txt
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest file 'kineticsTools.egg-info/SOURCES.txt'
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
Copying kineticsTools.egg-info to /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ipdSummary script to /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/bin
Installing summarizeModifications script to /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/python-kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/kineticstools/usr/bin
mv debian/python-kineticstools/usr/bin/* /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/kineticstools/usr/share/man//man1
rst2man doc/manual.rst > /<<BUILDDIR>>/kineticstools-0.5.2+dfsg/debian/kineticstools/usr/share/man//man1/ipdSummary.1
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-0.5.2+dfsg'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:322: renaming tree_predict.so to tree_predict.arm-linux-gnueabihf.so
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_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: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Versions}
dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Versions}
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-kineticstools-dbgsym' in '../python-kineticstools-dbgsym_0.5.2+dfsg-1_armhf.deb'.
dpkg-deb: building package 'python-kineticstools' in '../python-kineticstools_0.5.2+dfsg-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kineticstools_0.5.2+dfsg-1_armhf.changes
dpkg-genchanges: warning: package python-kineticstools-dbgsym listed in files list but not in control info
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build kineticstools-0.5.2+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160708-1152
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
kineticstools_0.5.2+dfsg-1_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Sat, 02 Jul 2016 19:59:45 -0700
Source: kineticstools
Binary: kineticstools kineticstools-data python-kineticstools
Architecture: armhf
Version: 0.5.2+dfsg-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@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)
Changes:
kineticstools (0.5.2+dfsg-1) unstable; urgency=medium
.
* Imported Upstream version 0.5.2+dfsg
(upstream git 9df3568 - 2016-03-22)
* Fix detection of compiled extension
* Refresh patches
* Bump minimum version of dependencies
* Bump Standards-Version to 3.9.8
* Globally use C.UTF-8 locale
* Enable build-time tests with respected exit code
* Set up autopkgtest
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Checksums-Sha256:
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Files:
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ae0e1906af7fc0a269118b6e789a243b 47582 python optional python-kineticstools_0.5.2+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python-kineticstools-dbgsym_0.5.2+dfsg-1_armhf.deb
--------------------------------------------------
new debian package, version 2.0.
size 5668 bytes: control archive=515 bytes.
483 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: python-kineticstools-dbgsym
Source: kineticstools
Version: 0.5.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18
Depends: python-kineticstools (= 0.5.2+dfsg-1)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/kineticsTools
Description: Debug symbols for python-kineticstools
Auto-Built-Package: debug-symbols
Build-Ids: c052b5455d9297c1183f2d1cf7de2e7b35fe76a0
drwxr-xr-x root/root 0 2016-07-08 11:52 ./
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/debug/.build-id/c0/
-rw-r--r-- root/root 7656 2016-07-08 11:52 ./usr/lib/debug/.build-id/c0/52b5455d9297c1183f2d1cf7de2e7b35fe76a0.debug
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/share/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-07-08 11:52 ./usr/share/doc/python-kineticstools-dbgsym -> python-kineticstools
python-kineticstools_0.5.2+dfsg-1_armhf.deb
-------------------------------------------
new debian package, version 2.0.
size 47582 bytes: control archive=2018 bytes.
1047 bytes, 20 lines control
3058 bytes, 31 lines md5sums
168 bytes, 9 lines * postinst #!/bin/sh
275 bytes, 14 lines * prerm #!/bin/sh
Package: python-kineticstools
Source: kineticstools
Version: 0.5.2+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 265
Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcommand, python-pbcore, python-scipy, python:any (>= 2.7.5-5~), kineticstools-data (= 0.5.2+dfsg-1)
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 2016-07-08 11:52 ./
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/bin/
-rw-r--r-- root/root 1829 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/bin/__init__.py
-rw-r--r-- root/root 4648 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/bin/copyIpdSummaryDataset.py
-rw-r--r-- root/root 2868 2016-07-08 11:40 ./usr/lib/python2.7/dist-packages/bin/testShared.py
-rw-r--r-- root/root 6577 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/bin/writeSummaryToCmp.py
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/
-rw-r--r-- root/root 1831 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/dependency_links.txt
-rw-r--r-- root/root 129 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/entry_points.txt
-rw-r--r-- root/root 1 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/not-zip-safe
-rw-r--r-- root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/requires.txt
-rw-r--r-- root/root 45 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools-0.5.2.egg-info/top_level.txt
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools/
-rw-r--r-- root/root 2638 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py
-rw-r--r-- root/root 35840 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py
-rw-r--r-- root/root 3628 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py
-rw-r--r-- root/root 12627 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py
-rw-r--r-- root/root 15729 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py
-rw-r--r-- root/root 6939 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py
-rw-r--r-- root/root 11759 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py
-rw-r--r-- root/root 4918 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py
-rw-r--r-- root/root 6268 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py
-rw-r--r-- root/root 34768 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py
-rw-r--r-- root/root 9249 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py
-rw-r--r-- root/root 1829 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/__init__.py
-rw-r--r-- root/root 22765 2016-07-08 11:40 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py
-rw-r--r-- root/root 30860 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py
-rw-r--r-- root/root 2182 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py
lrwxrwxrwx root/root 0 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools/resources -> ../../../../share/kineticstools/resources
-rw-r--r-- root/root 2399 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py
-rw-r--r-- root/root 7779 2016-03-22 20:00 ./usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py
-rw-r--r-- root/root 5464 2016-07-08 11:52 ./usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/share/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-07-08 11:52 ./usr/share/doc/python-kineticstools/
-rw-r--r-- root/root 503 2016-07-03 03:07 ./usr/share/doc/python-kineticstools/changelog.Debian.gz
-rw-r--r-- root/root 234 2016-03-22 20:00 ./usr/share/doc/python-kineticstools/changelog.gz
-rw-r--r-- root/root 2069 2016-03-16 05:54 ./usr/share/doc/python-kineticstools/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 326712
Build-Time: 690
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 630
Job: kineticstools_0.5.2+dfsg-1
Machine Architecture: armhf
Package: kineticstools
Package-Time: 1391
Source-Version: 0.5.2+dfsg-1
Space: 326712
Status: successful
Version: 0.5.2+dfsg-1
--------------------------------------------------------------------------------
Finished at 20160708-1152
Build needed 00:23:11, 326712k disc space