python-pbh5tools →
0.8.0+dfsg-4 →
armhf → 2016-02-22 13:42:13
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-04
+==============================================================================+
| python-pbh5tools 0.8.0+dfsg-4 (armhf) 22 Feb 2016 13:19 |
+==============================================================================+
Package: python-pbh5tools
Version: 0.8.0+dfsg-4
Source Version: 0.8.0+dfsg-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-edlWWW/python-pbh5tools-0.8.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-edlWWW' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-ea4efe93-d543-46ec-9234-e875bf4fe1c3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
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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 [8751 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.8 MB]
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| Fetch source files |
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Check APT
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Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-pbh5tools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/python-pbh5tools.git
Please use:
git clone git://anonscm.debian.org/debian-med/python-pbh5tools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 8559 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main python-pbh5tools 0.8.0+dfsg-4 (dsc) [2287 B]
Get:2 http://172.17.0.1/private stretch-staging/main python-pbh5tools 0.8.0+dfsg-4 (tar) [8550 kB]
Get:3 http://172.17.0.1/private stretch-staging/main python-pbh5tools 0.8.0+dfsg-4 (diff) [6140 B]
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Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-Z4aSmh/apt_archive/sbuild-build-depends-core-dummy.deb'.
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| Install core build dependencies (apt-based resolver) |
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 21 not upgraded.
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Merged Build-Depends: debhelper (>= 9), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-cram
Filtered Build-Depends: debhelper (>= 9), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-cram
dpkg-deb: building package 'sbuild-build-depends-python-pbh5tools-dummy' in '/<<BUILDDIR>>/resolver-knSR5Q/apt_archive/sbuild-build-depends-python-pbh5tools-dummy.deb'.
OK
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+------------------------------------------------------------------------------+
| Install python-pbh5tools build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autotools-dev bsdmainutils debhelper dh-python dh-strip-nondeterminism
docutils-common file fonts-font-awesome fonts-lato gettext gettext-base
groff-base intltool-debian libaec0 libarchive-zip-perl libblas-common
libblas3 libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libhdf5-10 libhts1 libicu55 libjs-jquery
libjs-modernizr libjs-sphinxdoc libjs-underscore liblapack3 libmagic1
libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libsqlite3-0 libssl1.0.2 libsz2 libunistring0 libxml2
man-db mime-support po-debconf python python-alabaster python-babel
python-babel-localedata python-cram python-docutils python-h5py
python-jinja2 python-markupsafe python-minimal python-nose python-numpy
python-pbcore python-pkg-resources python-pygments python-pysam python-roman
python-setuptools python-six python-sphinx python-sphinx-rtd-theme python-tz
python2.7 python2.7-minimal python3 python3-minimal python3.5
python3.5-minimal sgml-base sphinx-common sphinx-rtd-theme-common xml-core
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev groff 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-jinja2-doc python-coverage python-nose-doc gfortran python-dev
python-numpy-dbg python-numpy-doc python-pbcore-doc ttf-bitstream-vera
python-setuptools-doc libjs-mathjax dvipng texlive-latex-extra
texlive-fonts-recommended 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
javascript-common libmail-sendmail-perl python-pil libpaper-utils
docutils-doc python-chardet sphinx-doc
The following NEW packages will be installed:
autotools-dev bsdmainutils debhelper dh-python dh-strip-nondeterminism
docutils-common file fonts-font-awesome fonts-lato gettext gettext-base
groff-base intltool-debian libaec0 libarchive-zip-perl libblas-common
libblas3 libcroco3 libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libhdf5-10 libhts1 libicu55 libjs-jquery
libjs-modernizr libjs-sphinxdoc libjs-underscore liblapack3 libmagic1
libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal
libpython3.5-stdlib libsqlite3-0 libssl1.0.2 libsz2 libunistring0 libxml2
man-db mime-support po-debconf python python-alabaster python-babel
python-babel-localedata python-cram python-docutils python-h5py
python-jinja2 python-markupsafe python-minimal python-nose python-numpy
python-pbcore python-pkg-resources python-pygments python-pysam python-roman
python-setuptools python-six python-sphinx python-sphinx-rtd-theme python-tz
python2.7 python2.7-minimal python3 python3-minimal python3.5
python3.5-minimal sbuild-build-depends-python-pbh5tools-dummy sgml-base
sphinx-common sphinx-rtd-theme-common xml-core
0 upgraded, 81 newly installed, 0 to remove and 21 not upgraded.
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Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
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Get:59 http://172.17.0.1/private stretch-staging/main armhf python-babel-localedata all 1.3+dfsg.1-6 [1935 kB]
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Get:69 http://172.17.0.1/private stretch-staging/main armhf python-markupsafe armhf 0.23-2+b1 [15.7 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf python-jinja2 all 2.8-1 [111 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf python-nose all 1.3.7-1 [132 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf python-pysam armhf 0.8.4+ds-1 [716 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf python-pbcore all 1.2.7+dfsg-1 [9084 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf python-pygments all 2.1+dfsg-1 [533 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf python-setuptools all 18.8-1 [202 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf python-alabaster all 0.7.6-1 [15.9 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libjs-modernizr all 2.6.2+ds1-1 [71.3 kB]
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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_2.26-3 dpkg-dev_1.18.4 g++-5_5.3.1-8+rpi1 gcc-5_5.3.1-8+rpi1 libc6-dev_2.21-7 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.113+nmu3 apt_1.2.3 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-3 bsdmainutils_9.0.6 bsdutils_1:2.27.1-3 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.24-1 cpio_2.11+dfsg-4.1 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-8+rpi1 dash_0.5.8-2.1 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debianutils_4.7 dh-python_2.20151103 dh-strip-nondeterminism_0.015-1 diffutils_1:3.3-3 dmsetup_2:1.02.115-2 docutils-common_0.12+dfsg-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 fonts-font-awesome_4.5.0~dfsg-1 fonts-lato_2.0-1 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-8+rpi1 gcc_4:5.3.1-1+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_4.9.3-10 gcc-5_5.3.1-8+rpi1 gcc-5-base_5.3.1-8+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-1 gpgv_1.4.20-1 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 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libgcc-4.9-dev_4.9.3-10 libgcc-5-dev_5.3.1-8+rpi1 libgcc1_1:5.3.1-8+rpi1 libgcrypt20_1.6.4-5 libgdbm3_1.8.3-13.1 libgfortran3_5.3.1-8+rpi1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-8+rpi1 libgpg-error0_1.21-1 libhdf5-10_1.8.16+docs-3+b1 libhts1_1.3-1+rpi1 libicu55_55.1-7 libisl15_0.16.1-1 libjs-jquery_1.11.3+dfsg-4 libjs-modernizr_2.6.2+ds1-1 libjs-sphinxdoc_1.3.5-1 libjs-underscore_1.7.0~dfsg-1 libklibc_2.0.4-7+rpi1 libkmod2_22-1 liblapack3_3.6.0-2 liblz4-1_0.0~r131-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-3 libmpc3_1.0.3-1 libmpdec2_2.4.1-1 libmpfr4_3.1.3-2 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-1 libperl5.22_5.22.1-5 libpipeline1_1.4.1-2 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-3 libpython2.7-stdlib_2.7.11-3 libpython3-stdlib_3.5.1-1 libpython3.5-minimal_3.5.1-5 libpython3.5-stdlib_3.5.1-5 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-3 libsqlite3-0_3.10.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2f-2 libstdc++-4.9-dev_4.9.3-10 libstdc++-5-dev_5.3.1-8+rpi1 libstdc++6_5.3.1-8+rpi1 libsystemd0_228-6 libsz2_0.3.2-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-8+rpi1 libudev1_228-6 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-3 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-5 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-3 multiarch-support_2.21-7 nano_2.5.1-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-5 perl-base_5.22.1-5 perl-modules-5.22_5.22.1-7 po-debconf_1.0.19 procps_2:3.3.11-3 python_2.7.11-1 python-alabaster_0.7.6-1 python-babel_1.3+dfsg.1-6 python-babel-localedata_1.3+dfsg.1-6 python-cram_0.6-1 python-docutils_0.12+dfsg-1 python-h5py_2.6.0-1 python-jinja2_2.8-1 python-markupsafe_0.23-2+b1 python-minimal_2.7.11-1 python-nose_1.3.7-1 python-numpy_1:1.10.4-2 python-pbcore_1.2.7+dfsg-1 python-pkg-resources_18.8-1 python-pygments_2.1+dfsg-1 python-pysam_0.8.4+ds-1 python-roman_2.0.0-2 python-setuptools_18.8-1 python-six_1.10.0-2 python-sphinx_1.3.5-1 python-sphinx-rtd-theme_0.1.9-1 python-tz_2012c+dfsg-0.1 python2.7_2.7.11-3 python2.7-minimal_2.7.11-3 python3_3.5.1-1 python3-minimal_3.5.1-1 python3.5_3.5.1-5 python3.5-minimal_3.5.1-5 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pbh5tools-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sgml-base_1.26+nmu4 sphinx-common_1.3.5-1 sphinx-rtd-theme-common_0.1.9-1 startpar_0.59-3 systemd_228-6 systemd-sysv_228-6 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2016a-1 udev_228-6 util-linux_2.27.1-3 xml-core_0.13+nmu2 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
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gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Feb 15 07:44:13 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./python-pbh5tools_0.8.0+dfsg-4.dsc
dpkg-source: info: extracting python-pbh5tools in python-pbh5tools-0.8.0+dfsg
dpkg-source: info: unpacking python-pbh5tools_0.8.0+dfsg.orig.tar.gz
dpkg-source: info: unpacking python-pbh5tools_0.8.0+dfsg-4.debian.tar.xz
dpkg-source: info: applying default-doc-theme
dpkg-source: info: applying pbcore-change.patch
dpkg-source: info: applying verbose-testing.patch
dpkg-source: info: applying override-test-failure.patch
dpkg-source: info: applying ignore-cram-results.patch
dpkg-source: info: applying fix-type-in-test.patch
Check disc space
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Sufficient free space for build
User Environment
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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-ea4efe93-d543-46ec-9234-e875bf4fe1c3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package python-pbh5tools
dpkg-buildpackage: source version 0.8.0+dfsg-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build python-pbh5tools-0.8.0+dfsg
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
LC_ALL=C.UTF-8 dh clean --with python2 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_auto_clean
I: pybuild base:184: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/python-pbh5tools-0.8.0+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
/usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
cd doc && rm -rf modules.rst pbtools.* bash5lib.* cmph5tools.* \
bash5tools.* _templates _static _build searchindex.js objects.inv
rm -rf build/;\
find . -name "*.egg-info" | xargs rm -rf;\
find . -name "*.pyc" | xargs rm -rf;\
rm -rf dist/
rm -f nosetests.xml
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
LC_ALL=C.UTF-8 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
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_auto_build
I: pybuild base:184: /usr/bin/python setup.py build
running build
running build_py
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Compare.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Format.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Merge.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Select.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Sort.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Stats.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/CmpH5Utils.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/Indexer.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/Metrics.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/PBH5ToolsException.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/__init__.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/_version.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/cbook.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
copying ./pbh5tools/mlab.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools
running build_ext
building 'pbh5tools/ci' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/pbh5tools
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 pbh5tools/ci.c -o build/temp.linux-armv7l-2.7/pbh5tools/ci.o -O3 -shared
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/pbh5tools/ci.o -o /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/ci.so
running build_scripts
creating build/scripts-2.7
copying and adjusting bin/bash5tools.py -> build/scripts-2.7
copying and adjusting bin/cmph5tools.py -> build/scripts-2.7
changing mode of build/scripts-2.7/bash5tools.py from 664 to 775
changing mode of build/scripts-2.7/cmph5tools.py from 664 to 775
/usr/bin/make -C doc html
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc'
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v1.3.5
making output directory...
loading pickled environment... not yet created
loading intersphinx inventory from http://docs.python.org/objects.inv...
WARNING: intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to <class 'urllib2.URLError'>: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)>
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 2 source files that are out of date
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] cmph5tools-examples
reading sources... [100%] index
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 50%] cmph5tools-examples
writing output... [100%] index
generating indices... genindex
writing additional pages... search
copying static files... WARNING: html_static_path entry u'/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 2 warnings.
Build finished. The HTML pages are in _build/html.
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/doc'
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="PATH=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7:$PATH /usr/bin/make test" \
dh_auto_test
I: pybuild base:184: PATH=/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/build/scripts-2.7:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make test
make[2]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
cram -v doc/examples.t
doc/examples.t: failed
--- examples.t
+++ examples.t.err
@@ -20,16 +20,16 @@
$ cmph5tools.py stats --what "Tbl(q = Percentile(ReadLength, 90), m = Median(Accuracy))" \
> --groupBy Barcode $INCMP | tail
- F_44--R_44 516.80 0.90
- F_45--R_45 534.60 0.90
- F_46--R_46 517.80 0.90
- F_47--R_47 515.80 0.91
- F_48--R_48 624.20 0.91
- F_5--R_5 571.60 0.90
- F_6--R_6 507.90 0.90
- F_7--R_7 572.40 0.90
- F_8--R_8 574.40 0.91
- F_9--R_9 485.60 0.90
+ F_44--R_44 516.80 0.90
+ F_45--R_45 534.60 0.90
+ F_46--R_46 517.80 0.90
+ F_47--R_47 515.80 0.91
+ F_48--R_48 624.20 0.91
+ F_5--R_5 571.60 0.90
+ F_6--R_6 507.90 0.90
+ F_7--R_7 572.40 0.90
+ F_8--R_8 574.40 0.91
+ F_9--R_9 485.60 0.90
## Example 3: query the package to determine the available metrics and statistics
@@ -85,24 +85,24 @@
$ cmph5tools.py stats --what "Tbl(a=Accuracy,b=Barcode)" \
> --where "Barcode == 'F_28--R_28'" \
> --groupBy Reference $INCMP
- Group a b
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.95 F_28--R_28
- EGFR_600_t29_1 0.93 F_28--R_28
- EGFR_600_t29_1 0.91 F_28--R_28
- EGFR_600_t29_1 0.90 F_28--R_28
- EGFR_600_t29_1 0.94 F_28--R_28
- EGFR_600_t29_1 0.93 F_28--R_28
- EGFR_600_t9_1 0.86 F_28--R_28
+ Group a b
+ EGFR_600_t29_1 0.91 F_28--R_28
+ EGFR_600_t29_1 0.91 F_28--R_28
+ EGFR_600_t29_1 0.95 F_28--R_28
+ EGFR_600_t29_1 0.93 F_28--R_28
+ EGFR_600_t29_1 0.91 F_28--R_28
+ EGFR_600_t29_1 0.90 F_28--R_28
+ EGFR_600_t29_1 0.94 F_28--R_28
+ EGFR_600_t29_1 0.93 F_28--R_28
+ EGFR_600_t9_1 0.86 F_28--R_28
## Example 5: Familiar SQL-like functions
$ cmph5tools.py stats --what "Count(Reference)" \
> --where "Barcode == 'F_10--R_10'" \
> --groupBy Reference $INCMP
- Group Count(Reference)
- EGFR_600_t11_1 62
+ Group Count(Reference)
+ EGFR_600_t11_1 62
## Handling IPD, PulseWidth, and Base-level Metrics
@@ -144,14 +144,14 @@
avg acc: 0.9658
\t Movie Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
m121005_190843_42142_c100376662550000001523029810101285_s1_p0 4770 1.0 170.4
m121005_190843_42142_c100376662550000001523029810101285_s2_p0 2259 1.0 173.8
m121005_210848_42142_c100376662550000001523029810101286_s1_p0 6167 1.0 192.7
m121005_210848_42142_c100376662550000001523029810101286_s2_p0 2119 1.0 117.7
\t Reference Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
EGFR_600_t11_1 1396 1.0 232.7
EGFR_600_t13_1 83 1.0 41.5
EGFR_600_t15_1 252 1.0 126.0
@@ -173,7 +173,7 @@
EGFR_600_t6_1 201 1.0 50.2
EGFR_600_t7_1 873 1.0 436.5
EGFR_600_t9_1 562 1.0 112.4
- MET_600_t2_1 42 1.0 42.0
+ MET_600_t2_1 42 1.0 42.0
MET_600_t2_11 681 1.0 227.0
MET_600_t2_13 448 1.0 448.0
MET_600_t2_14 223 1.0 223.0
@@ -182,25 +182,25 @@
MET_600_t2_17 44 1.0 44.0
MET_600_t2_18 701 1.0 175.2
MET_600_t2_19 546 1.0 182.0
- MET_600_t2_2 186 1.0 93.0
+ MET_600_t2_2 186 1.0 93.0
MET_600_t2_20 394 1.0 98.5
MET_600_t2_21 71 1.0 35.5
- MET_600_t2_3 655 1.0 218.3
- MET_600_t2_4 1321 1.0 330.2
- MET_600_t2_5 500 1.0 500.0
- MET_600_t2_6 120 1.0 120.0
- MET_600_t2_7 660 1.0 220.0
- MET_600_t2_8 24 1.0 24.0
- MET_600_t2_9 67 1.0 67.0
+ MET_600_t2_3 655 1.0 218.3
+ MET_600_t2_4 1321 1.0 330.2
+ MET_600_t2_5 500 1.0 500.0
+ MET_600_t2_6 120 1.0 120.0
+ MET_600_t2_7 660 1.0 220.0
+ MET_600_t2_8 24 1.0 24.0
+ MET_600_t2_9 67 1.0 67.0
## Selection
$ cmph5tools.py select --groupBy Barcode \
> --where "(Barcode == 'F_42--R_42') | (Barcode == 'F_10--R_10')" $INCMP
$ cmph5tools.py merge --outFile merged.cmp.h5 F_42--R_42.cmp.h5 F_10--R_10.cmp.h5
$ cmph5tools.py stats --what "Count(Reference)" --groupBy Barcode merged.cmp.h5
- Group Count(Reference)
- F_10--R_10 62
- F_42--R_42 76
+ Group Count(Reference)
+ F_10--R_10 62
+ F_42--R_42 76
cmp.h5 files can also be split by a pre-defined csv file with three columns.
# Ran 1 tests, 0 skipped, 1 failed.
Makefile:26: recipe for target 'examples' failed
make[2]: [examples] Error 1 (ignored)
sed 's/^ / /' doc/examples.t > doc/examples.md
find tests -name "*.py" | xargs nosetests -v
test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Merge) ... ok
test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Select) ... ok
test_output_file_in_inputs (test_cmph5lib_CmpH5Merge.TestMergeException) ... ok
test_cmph5lib_CmpH5Sort.TestCmpH5Format.test___init__ ... ok
test_cmph5lib_CmpH5Sort.TestComputeIndices.test_compute_indices ... ok
test_cmph5lib_CmpH5Sort.TestComputeIndicesDP.test_compute_indices_d_p ... ok
test_cmph5lib_CmpH5Sort.TestComputeRefIndexTable.test_compute_ref_index_table ... ok
test_cmph5lib_CmpH5Sort.TestGetOverlappingRanges.test_get_overlapping_ranges ... ok
test_cmph5lib_CmpH5Sort.TestGetReadsInRange.test_get_reads_in_range ... ok
test_cmph5lib_CmpH5Sort.TestNumberWithinRange.test_number_within_range ... ok
----------------------------------------------------------------------
Ran 10 tests in 48.060s
OK
find tests/cram -name "*.t" | xargs cram -v
tests/cram/bash5tools.t: passed
tests/cram/groupcsv.t: passed
tests/cram/merge.t: passed
tests/cram/select.t: passed
tests/cram/sort-extended.t: passed
tests/cram/sort.t: passed
tests/cram/stats.t: failed
--- stats.t
+++ stats.t.err
@@ -26,7 +26,7 @@
481.80 0.83
Access movie name for each alignment
$ $CMD --what "Movie" --limit 5
- Movie
+ Movie
m110818_075520_42141_c100129202555500000315043109121112_s2_p0
m110818_075520_42141_c100129202555500000315043109121112_s2_p0
m110818_075520_42141_c100129202555500000315043109121112_s1_p0
@@ -38,24 +38,24 @@
547.80 0.84
Aggregate statistics grouped by movie
$ $CMD --what "Tbl(mrl = Percentile(ReadLength, 90), macc = Mean(Accuracy))" --groupBy "Movie"
- Group mrl macc
+ Group mrl macc
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 547.80 0.84
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 445.20 0.83
Aggregate statistics grouped by multiple factors
$ $CMD --what "Tbl(mrl = Percentile(ReadLength, 90), macc = Mean(Accuracy))" --groupBy "Movie * Reference"
- Group mrl macc
+ Group mrl macc
m110818_075520_42141_c100129202555500000315043109121112_s1_p0:lambda_NEB3011 547.80 0.84
m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011 445.20 0.83
Per-alignment metrics grouped by multiple factors
$ $CMD --what "Tbl(readlength = ReadLength, errorRate = 1 - Accuracy, ipd = Mean(IPD))" --groupBy "Movie * Reference" --limit 2
- Group readlength errorRate ipd
+ Group readlength errorRate ipd
m110818_075520_42141_c100129202555500000315043109121112_s1_p0:lambda_NEB3011 342 0.13 0.18
m110818_075520_42141_c100129202555500000315043109121112_s1_p0:lambda_NEB3011 254 0.18 0.25
m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011 301 0.16 0.21
m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011 404 0.18 0.28
Per-alignment metrics grouped and filtered
$ $CMD --what "Tbl(readlength = ReadLength, errorRate = 1 - Accuracy, ipd = Mean(IPD), holeNumber = HoleNumber)" --groupBy "Movie * Reference" --where "HoleNumber != 9" --limit 2
- Group readlength errorRate ipd holeNumber
+ Group readlength errorRate ipd holeNumber
m110818_075520_42141_c100129202555500000315043109121112_s1_p0:lambda_NEB3011 342 0.13 0.18 2001
m110818_075520_42141_c100129202555500000315043109121112_s1_p0:lambda_NEB3011 254 0.18 0.25 2001
m110818_075520_42141_c100129202555500000315043109121112_s2_p0:lambda_NEB3011 301 0.16 0.21 3008
@@ -96,11 +96,11 @@
avg acc: 0.7942
\t Movie Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 666 0.8 222.0
\t Reference Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
lambda_NEB3011 666 0.8 222.0
----------------------------------------
filename: m110818_075520_42141_c100129202555500000315043109121112_s2_p0.cmp.h5
@@ -113,11 +113,11 @@
avg acc: 0.7943
\t Movie Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 676 0.8 225.3
\t Reference Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
lambda_NEB3011 676 0.8 225.3
Make new cmp.h5 with subset of indexed alignments
$ $SCMD --idx 1 2 3 4 --outFile 1234.cmp.h5
@@ -133,12 +133,12 @@
avg acc: 0.8391
\t Movie Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 863 0.8 287.7
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 404 0.8 404.0
\t Reference Summary: (esc)
- Group nBases avgAccuracy avgReadLength
+ Group nBases avgAccuracy avgReadLength
lambda_NEB3011 1267 0.8 316.8
Check that default 'what' clause prints readlength and accuracy (all reads)
$ cmph5tools.py stats $INH5 --limit 5
@@ -173,24 +173,24 @@
257 0.84
Check sortBy and grouping (no aggregate)
$ $CMD --what "(Accuracy, )" --sortBy ReadLength --groupBy Movie --limit 2
- Group 1.0-NErrors/ReadLength*1.0
+ Group 1.0-NErrors/ReadLength*1.0
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 0.84
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 0.80
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 0.79
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 0.81
Check sortBy and grouping (with aggregate)
$ $CMD --what "(Mean(Accuracy), )" --sortBy ReadLength --groupBy Movie
- Group Mean(1.0-NErrors/ReadLength*1.0)
+ Group Mean(1.0-NErrors/ReadLength*1.0)
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 0.84
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 0.83
Check arithmetic in what clause
$ $CMD --what "(Mean(100* Accuracy)/Sum(Accuracy), )" --sortBy ReadLength --groupBy Movie
- Group Mean(100*1.0-NErrors/ReadLength*1.0)/Sum(1.0-NErrors/ReadLength*1.0)
+ Group Mean(100*1.0-NErrors/ReadLength*1.0)/Sum(1.0-NErrors/ReadLength*1.0)
m110818_075520_42141_c100129202555500000315043109121112_s1_p0 2.56
m110818_075520_42141_c100129202555500000315043109121112_s2_p0 2.22
Output columns from tuple and group by multiple factors (sorting within group)
$ $CMD --what "(Sum(ReadLength), Mean(Accuracy))" --sortBy ReadLength --groupBy HoleNumber*Movie --limit 1
- Group Mean(1.0-NErrors/ReadLength*1.0) Sum(ReadLength)
+ Group Mean(1.0-NErrors/ReadLength*1.0) Sum(ReadLength)
1000:m110818_075520_42141_c100129202555500000315043109121112_s1_p0 0.84 188
1000:m110818_075520_42141_c100129202555500000315043109121112_s2_p0 0.82 674
1002:m110818_075520_42141_c100129202555500000315043109121112_s2_p0 0.87 117
tests/cram/valid.t: passed
# Ran 8 tests, 0 skipped, 1 failed.
Makefile:20: recipe for target 'test' failed
make[2]: [test] Error 123 (ignored)
make[2]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
fakeroot debian/rules binary-arch
LC_ALL=C.UTF-8 dh binary-arch --with python2 --buildsystem=pybuild
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py install --root /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools
running install
running build
running build_py
running build_ext
running build_scripts
running install_lib
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Compare.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Format.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Merge.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Select.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Sort.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Stats.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Utils.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/Indexer.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/Metrics.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/PBH5ToolsException.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/__init__.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/_version.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/cbook.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/mlab.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/ci.so -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/__init__.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/PBH5ToolsException.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Select.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Format.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Utils.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/Metrics.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Merge.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Sort.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Stats.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/mlab.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/cbook.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/CmpH5Compare.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/_version.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
copying /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/.pybuild/pythonX.Y_2.7/build/pbh5tools/Indexer.pyc -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools
running install_egg_info
running egg_info
creating pbh5tools.egg-info
writing requirements to pbh5tools.egg-info/requires.txt
writing pbh5tools.egg-info/PKG-INFO
writing top-level names to pbh5tools.egg-info/top_level.txt
writing dependency_links to pbh5tools.egg-info/dependency_links.txt
writing manifest file 'pbh5tools.egg-info/SOURCES.txt'
reading manifest file 'pbh5tools.egg-info/SOURCES.txt'
writing manifest file 'pbh5tools.egg-info/SOURCES.txt'
Copying pbh5tools.egg-info to /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info
Skipping SOURCES.txt
running install_scripts
creating /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin
copying build/scripts-2.7/bash5tools.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin
copying build/scripts-2.7/cmph5tools.py -> /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin
changing mode of /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin/bash5tools.py to 775
changing mode of /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin/cmph5tools.py to 775
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_install
# We do this here rather than in .install files so that debhelper
# takes care of the #!/usr/bin/env lines for us
mkdir -p /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/pbh5tools/usr/bin
mv debian/python-pbh5tools/usr/bin/bash5tools.py /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/pbh5tools/usr/bin/bash5tools
mv debian/python-pbh5tools/usr/bin/cmph5tools.py /<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg/debian/pbh5tools/usr/bin/cmph5tools
make[1]: Leaving directory '/<<BUILDDIR>>/python-pbh5tools-0.8.0+dfsg'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_installexamples -a -O--buildsystem=pybuild
dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:328: renaming ci.so to ci.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-pbh5tools/usr/lib/python2.7/dist-packages/pbh5tools/ci.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-pbh5tools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-pbh5tools: unused substitution variable ${python:Versions}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-pbh5tools: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-pbh5tools: unused substitution variable ${python:Versions}
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-pbh5tools-dbgsym' in '../python-pbh5tools-dbgsym_0.8.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'python-pbh5tools' in '../python-pbh5tools_0.8.0+dfsg-4_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pbh5tools_0.8.0+dfsg-4_armhf.changes
dpkg-genchanges: warning: package python-pbh5tools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build python-pbh5tools-0.8.0+dfsg
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160222-1338
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
python-pbh5tools_0.8.0+dfsg-4_armhf.changes:
--------------------------------------------
Format: 1.8
Date: Sun, 14 Feb 2016 23:13:52 -0800
Source: python-pbh5tools
Binary: pbh5tools python-pbh5tools python-pbh5tools-doc
Architecture: armhf
Version: 0.8.0+dfsg-4
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@ghraoui.name>
Description:
pbh5tools - tools for manipulating Pacific Biosciences HDF5 files
python-pbh5tools - tools for manipulating Pacific Biosciences HDF5 files -- Python 2
python-pbh5tools-doc - tools for manipulating HDF5 files produced by Pacific Biosciences
Closes: 814210
Changes:
python-pbh5tools (0.8.0+dfsg-4) unstable; urgency=medium
.
* Split command-line executables into a separate binary package
* Fix broken unit test (Closes: #814210)
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Checksums-Sha256:
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Files:
840eb4a070d9b9bd1f7b384407cadb1e 5260 debug extra python-pbh5tools-dbgsym_0.8.0+dfsg-4_armhf.deb
273383948baf1af1465fcade12740491 28362 python optional python-pbh5tools_0.8.0+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python-pbh5tools-dbgsym_0.8.0+dfsg-4_armhf.deb
----------------------------------------------
new debian package, version 2.0.
size 5260 bytes: control archive=504 bytes.
470 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: python-pbh5tools-dbgsym
Source: python-pbh5tools
Version: 0.8.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18
Depends: python-pbh5tools (= 0.8.0+dfsg-4)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/pbh5tools
Description: Debug symbols for python-pbh5tools
Auto-Built-Package: debug-symbols
Build-Ids: db9352bbc5a1dc97796a3a866a127d87ec8ea475
drwxr-xr-x root/root 0 2016-02-22 13:38 ./
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/debug/.build-id/db/
-rw-r--r-- root/root 7336 2016-02-22 13:38 ./usr/lib/debug/.build-id/db/9352bbc5a1dc97796a3a866a127d87ec8ea475.debug
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-02-22 13:38 ./usr/share/doc/python-pbh5tools-dbgsym -> python-pbh5tools
python-pbh5tools_0.8.0+dfsg-4_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 28362 bytes: control archive=1617 bytes.
828 bytes, 17 lines control
2206 bytes, 24 lines md5sums
164 bytes, 9 lines * postinst #!/bin/sh
267 bytes, 14 lines * prerm #!/bin/sh
Package: python-pbh5tools
Version: 0.8.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 135
Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcore, python:any (>= 2.7.5-5~)
Section: python
Priority: optional
Homepage: https://github.com/PacificBiosciences/pbh5tools
Description: tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
This package provides functionality for manipulating and extracting data
from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
cmp.h5 files contain alignment information while bas.h5 files contain
base-call information.
.
pbh5tools is part of the SMRTAnalysis suite. This package provides the
Python 2 backend library
drwxr-xr-x root/root 0 2016-02-22 13:38 ./
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/
-rw-r--r-- root/root 1827 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/dependency_links.txt
-rw-r--r-- root/root 1 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/not-zip-safe
-rw-r--r-- root/root 0 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/requires.txt
-rw-r--r-- root/root 23 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/top_level.txt
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools/
-rw-r--r-- root/root 4088 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Compare.py
-rw-r--r-- root/root 4252 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Format.py
-rw-r--r-- root/root 14153 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Merge.py
-rw-r--r-- root/root 7366 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Select.py
-rw-r--r-- root/root 20340 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Sort.py
-rw-r--r-- root/root 3425 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Stats.py
-rw-r--r-- root/root 3379 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/CmpH5Utils.py
-rw-r--r-- root/root 3525 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/Indexer.py
-rw-r--r-- root/root 19047 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/Metrics.py
-rw-r--r-- root/root 2076 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/PBH5ToolsException.py
-rw-r--r-- root/root 0 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/__init__.py
-rw-r--r-- root/root 1852 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/_version.py
-rw-r--r-- root/root 3469 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/cbook.py
-rw-r--r-- root/root 5468 2016-02-22 13:38 ./usr/lib/python2.7/dist-packages/pbh5tools/ci.arm-linux-gnueabihf.so
-rw-r--r-- root/root 11874 2015-08-15 19:12 ./usr/lib/python2.7/dist-packages/pbh5tools/mlab.py
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/doc/python-pbh5tools/
-rw-r--r-- root/root 248 2016-02-15 07:33 ./usr/share/doc/python-pbh5tools/NEWS.Debian.gz
-rw-r--r-- root/root 574 2016-02-15 07:33 ./usr/share/doc/python-pbh5tools/changelog.Debian.gz
-rw-r--r-- root/root 1977 2016-02-15 07:33 ./usr/share/doc/python-pbh5tools/copyright
drwxr-xr-x root/root 0 2016-02-22 13:38 ./usr/share/doc/python-pbh5tools/examples/
-rw-r--r-- root/root 3058 2016-02-22 13:33 ./usr/share/doc/python-pbh5tools/examples/examples.md.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 11424
Build-Time: 525
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 543
Job: python-pbh5tools_0.8.0+dfsg-4
Machine Architecture: armhf
Package: python-pbh5tools
Package-Time: 1117
Source-Version: 0.8.0+dfsg-4
Space: 11424
Status: successful
Version: 0.8.0+dfsg-4
--------------------------------------------------------------------------------
Finished at 20160222-1338
Build needed 00:18:37, 11424k disc space