python-pbh5tools →
0.8.0+dfsg-3 →
armhf → 2015-12-04 11:48:47
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testwandboard
╔══════════════════════════════════════════════════════════════════════════════╗
║ python-pbh5tools 0.8.0+dfsg-3 (armhf) 04 Dec 2015 11:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: python-pbh5tools
Version: 0.8.0+dfsg-3
Source Version: 0.8.0+dfsg-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-pqPtWw/python-pbh5tools-0.8.0+dfsg' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/python-pbh5tools-pqPtWw' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-5d46c282-3796-433a-80ed-b2cb0486e5d8' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8506 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.5 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 19.0 MB in 36s (521 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'python-pbh5tools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/python-pbh5tools.git
Need to get 8558 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main python-pbh5tools 0.8.0+dfsg-3 (dsc) [2235 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main python-pbh5tools 0.8.0+dfsg-3 (tar) [8550 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main python-pbh5tools 0.8.0+dfsg-3 (diff) [5540 B]
Fetched 8558 kB in 4s (1729 kB/s)
Download complete and in download only mode
Check architectures
───────────────────
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-IYNfdD/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 21 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12041 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) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-python, python, python-setuptools, python-pbcore, python-sphinx, python-nose, python-cram
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), 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-7I80Vv/apt_archive/sbuild-build-depends-python-pbh5tools-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install python-pbh5tools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
bsdmainutils cpp-5 debhelper dh-python dh-strip-nondeterminism
docutils-common file fonts-font-awesome fonts-lato g++-5 gcc-5 gcc-5-base
gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan2
libatomic1 libblas-common libblas3 libcc1-0 libcroco3 libexpat1 libffi6
libfile-stripnondeterminism-perl libgcc-5-dev libgcc1 libgfortran3
libglib2.0-0 libgomp1 libhdf5-10 libhts1 libicu55 libisl15 libjs-jquery
libjs-modernizr libjs-sphinxdoc libjs-underscore liblapack3 libmagic1
libmpdec2 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.4-minimal
libpython3.4-stdlib libsqlite3-0 libssl1.0.2 libstdc++-5-dev libstdc++6
libtimedate-perl libubsan0 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 python3.4 python3.4-minimal sgml-base sphinx-common
sphinx-rtd-theme-common xml-core
Suggested packages:
wamerican wordlist whois vacation gcc-5-locales dh-make gcc-5-doc
libstdc++6-5-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
libmpx0-dbg libquadmath-dbg gettext-doc autopoint libasprintf-dev
libgettextpo-dev groff libstdc++-5-doc 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 python3.4-venv python3.4-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:
bsdmainutils debhelper dh-python dh-strip-nondeterminism docutils-common
file fonts-font-awesome fonts-lato gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libblas-common libblas3 libcroco3
libexpat1 libffi6 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0
libhdf5-10 libhts1 libicu55 libisl15 libjs-jquery libjs-modernizr
libjs-sphinxdoc libjs-underscore liblapack3 libmagic1 libmpdec2 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.2
libtimedate-perl 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 python3.4 python3.4-minimal
sbuild-build-depends-python-pbh5tools-dummy sgml-base sphinx-common
sphinx-rtd-theme-common xml-core
The following packages will be upgraded:
cpp-5 g++-5 gcc-5 gcc-5-base libasan2 libatomic1 libcc1-0 libgcc-5-dev
libgcc1 libgomp1 libstdc++-5-dev libstdc++6 libubsan0
13 upgraded, 80 newly installed, 0 to remove and 8 not upgraded.
Need to get 129 MB/129 MB of archives.
After this operation, 176 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libgomp1 armhf 5.2.1-23+rpi1+b1 [47.4 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main libatomic1 armhf 5.2.1-23+rpi1+b1 [6606 B]
Get:3 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.2.1-23+rpi1+b1 [167 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libgcc1 armhf 1:5.2.1-23+rpi1+b1 [38.5 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasan2 armhf 5.2.1-23+rpi1+b1 [227 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libubsan0 armhf 5.2.1-23+rpi1+b1 [84.3 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libisl15 armhf 0.15-3 [397 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main cpp-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libcc1-0 armhf 5.2.1-23+rpi1+b1 [24.7 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main g++-5 armhf 5.2.1-23+rpi1+b1 [32.0 MB]
Get:11 http://172.17.0.1/private/ stretch-staging/main gcc-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libgcc-5-dev armhf 5.2.1-23+rpi1+b1 [449 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libstdc++-5-dev armhf 5.2.1-23+rpi1+b1 [1428 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libstdc++6 armhf 5.2.1-23+rpi1+b1 [327 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-4 [1084 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-5+b1 [380 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-5+b1 [1092 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.9.2-1 [404 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libssl1.0.2 armhf 1.0.2d-3 [881 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-5+b1 [1811 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-5+b1 [265 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main fonts-lato all 2.0-1 [2684 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libmpdec2 armhf 2.4.1-1 [65.8 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libpython3.4-minimal armhf 3.4.3-10+b1 [493 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main python3.4-minimal armhf 3.4.3-10+b1 [1266 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main python3-minimal armhf 3.4.3-7 [35.1 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libpython3.4-stdlib armhf 3.4.3-10+b1 [2055 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main python3.4 armhf 3.4.3-10+b1 [227 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libpython3-stdlib armhf 3.4.3-7 [18.4 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main dh-python all 2.20151103 [76.9 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main python3 armhf 3.4.3-7 [21.3 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main sgml-base all 1.26+nmu4 [14.6 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libtimedate-perl all 2.3000-2 [42.2 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:57 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main xml-core all 0.13+nmu2 [24.2 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main docutils-common all 0.12+dfsg-1 [185 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main fonts-font-awesome all 4.4.0~dfsg-1 [493 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libblas-common armhf 1.2.20110419-11 [8490 B]
Get:62 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.2.1-23+rpi1+b1 [154 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main libblas3 armhf 1.2.20110419-11 [118 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main libhdf5-10 armhf 1.8.15-patch1+docs-5 [973 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libhts1 armhf 1.2.1-1+rpi1 [190 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main libjs-jquery all 1.11.3+dfsg-4 [163 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libjs-underscore all 1.7.0~dfsg-1 [49.9 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libjs-sphinxdoc all 1.3.1-8 [53.1 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main liblapack3 armhf 3.5.0-5 [1294 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main python-babel-localedata all 1.3+dfsg.1-6 [1935 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main python-pkg-resources all 18.4-2 [99.4 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main python-six all 1.10.0-1 [14.1 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main python-tz all 2012c+dfsg-0.1 [31.9 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main python-babel all 1.3+dfsg.1-6 [73.5 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main python-cram all 0.6-1 [13.1 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main python-roman all 2.0.0-2 [8130 B]
Get:77 http://172.17.0.1/private/ stretch-staging/main python-docutils all 0.12+dfsg-1 [361 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main python-numpy armhf 1:1.9.2-5 [1511 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main python-h5py armhf 2.5.0-1+b1 [440 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main python-markupsafe armhf 0.23-2 [15.6 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main python-jinja2 all 2.8-1 [111 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main python-nose all 1.3.6-1 [132 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main python-pysam armhf 0.8.4+ds-1 [716 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main python-pbcore all 1.2.6+dfsg-1 [9090 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main python-pygments all 2.0.1+dfsg-1.1 [481 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main python-setuptools all 18.4-2 [201 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main python-alabaster all 0.7.6-1 [15.9 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main libjs-modernizr all 2.6.2+ds1-1 [71.3 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main sphinx-rtd-theme-common all 0.1.9-1 [210 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main python-sphinx-rtd-theme all 0.1.9-1 [14.6 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main sphinx-common all 1.3.1-8 [320 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main python-sphinx all 1.3.1-8 [352 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 129 MB in 1min 18s (1654 kB/s)
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12041 files and directories currently installed.)
Preparing to unpack .../libgomp1_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgomp1:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libatomic1_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libatomic1:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../gcc-5-base_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking gcc-5-base:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up gcc-5-base:armhf (5.2.1-23+rpi1+b1) ...
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12042 files and directories currently installed.)
Preparing to unpack .../libgcc1_1%3a5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgcc1:armhf (1:5.2.1-23+rpi1+b1) over (1:5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libgcc1:armhf (1:5.2.1-23+rpi1+b1) ...
Processing triggers for libc-bin (2.19-22) ...
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12042 files and directories currently installed.)
Preparing to unpack .../libasan2_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libasan2:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libubsan0_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libubsan0:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Selecting previously unselected package libisl15:armhf.
Preparing to unpack .../libisl15_0.15-3_armhf.deb ...
Unpacking libisl15:armhf (0.15-3) ...
Preparing to unpack .../cpp-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking cpp-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libcc1-0_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libcc1-0:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../g++-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking g++-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../gcc-5_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking gcc-5 (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libgcc-5-dev_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgcc-5-dev:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libstdc++-5-dev_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libstdc++-5-dev:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Preparing to unpack .../libstdc++6_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libstdc++6:armhf (5.2.1-23+rpi1+b1) over (5.2.1-23+rpi1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libstdc++6:armhf (5.2.1-23+rpi1+b1) ...
Processing triggers for libc-bin (2.19-22) ...
Selecting previously unselected package groff-base.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12048 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-4_armhf.deb ...
Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.6_armhf.deb ...
Unpacking bsdmainutils (9.0.6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../libpython2.7-minimal_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.10-5+b1) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../python2.7-minimal_2.7.10-5+b1_armhf.deb ...
Unpacking python2.7-minimal (2.7.10-5+b1) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../python-minimal_2.7.9-1_armhf.deb ...
Unpacking python-minimal (2.7.9-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.59_all.deb ...
Unpacking mime-support (3.59) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.1.0-7_armhf.deb ...
Unpacking libexpat1:armhf (2.1.0-7) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-3_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-3) ...
Selecting previously unselected package libsqlite3-0:armhf.
Preparing to unpack .../libsqlite3-0_3.9.2-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.9.2-1) ...
Selecting previously unselected package libssl1.0.2:armhf.
Preparing to unpack .../libssl1.0.2_1.0.2d-3_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2d-3) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../libpython2.7-stdlib_2.7.10-5+b1_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.10-5+b1) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.10-5+b1_armhf.deb ...
Unpacking python2.7 (2.7.10-5+b1) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../libpython-stdlib_2.7.9-1_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.9-1) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libpython2.7-minimal:armhf (2.7.10-5+b1) ...
Setting up python2.7-minimal (2.7.10-5+b1) ...
Setting up python-minimal (2.7.9-1) ...
Selecting previously unselected package python.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13416 files and directories currently installed.)
Preparing to unpack .../python_2.7.9-1_armhf.deb ...
Unpacking python (2.7.9-1) ...
Selecting previously unselected package fonts-lato.
Preparing to unpack .../fonts-lato_2.0-1_all.deb ...
Unpacking fonts-lato (2.0-1) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../libmpdec2_2.4.1-1_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.1-1) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libpython3.4-minimal:armhf.
Preparing to unpack .../libpython3.4-minimal_3.4.3-10+b1_armhf.deb ...
Unpacking libpython3.4-minimal:armhf (3.4.3-10+b1) ...
Selecting previously unselected package python3.4-minimal.
Preparing to unpack .../python3.4-minimal_3.4.3-10+b1_armhf.deb ...
Unpacking python3.4-minimal (3.4.3-10+b1) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../python3-minimal_3.4.3-7_armhf.deb ...
Unpacking python3-minimal (3.4.3-7) ...
Selecting previously unselected package libpython3.4-stdlib:armhf.
Preparing to unpack .../libpython3.4-stdlib_3.4.3-10+b1_armhf.deb ...
Unpacking libpython3.4-stdlib:armhf (3.4.3-10+b1) ...
Selecting previously unselected package python3.4.
Preparing to unpack .../python3.4_3.4.3-10+b1_armhf.deb ...
Unpacking python3.4 (3.4.3-10+b1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../libpython3-stdlib_3.4.3-7_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.4.3-7) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../dh-python_2.20151103_all.deb ...
Unpacking dh-python (2.20151103) ...
Setting up libssl1.0.2:armhf (1.0.2d-3) ...
Setting up libpython3.4-minimal:armhf (3.4.3-10+b1) ...
Setting up libexpat1:armhf (2.1.0-7) ...
Setting up python3.4-minimal (3.4.3-10+b1) ...
Setting up python3-minimal (3.4.3-7) ...
Processing triggers for libc-bin (2.19-22) ...
Selecting previously unselected package python3.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14420 files and directories currently installed.)
Preparing to unpack .../python3_3.4.3-7_armhf.deb ...
Unpacking python3 (3.4.3-7) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../sgml-base_1.26+nmu4_all.deb ...
Unpacking sgml-base (1.26+nmu4) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_armhf.deb ...
Unpacking gettext-base (0.19.6-1) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-6_armhf.deb ...
Unpacking libicu55:armhf (55.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_armhf.deb ...
Unpacking libxml2:armhf (2.9.2+zdfsg1-4) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.46.2-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.46.2-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.9-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.9-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_armhf.deb ...
Unpacking gettext (0.19.6-1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.18_all.deb ...
Unpacking po-debconf (1.0.18) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ...
Unpacking libarchive-zip-perl (1.53-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20151005_all.deb ...
Unpacking debhelper (9.20151005) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../xml-core_0.13+nmu2_all.deb ...
Unpacking xml-core (0.13+nmu2) ...
Selecting previously unselected package docutils-common.
Preparing to unpack .../docutils-common_0.12+dfsg-1_all.deb ...
Unpacking docutils-common (0.12+dfsg-1) ...
Selecting previously unselected package fonts-font-awesome.
Preparing to unpack .../fonts-font-awesome_4.4.0~dfsg-1_all.deb ...
Unpacking fonts-font-awesome (4.4.0~dfsg-1) ...
Selecting previously unselected package libblas-common.
Preparing to unpack .../libblas-common_1.2.20110419-11_armhf.deb ...
Unpacking libblas-common (1.2.20110419-11) ...
Selecting previously unselected package libgfortran3:armhf.
Preparing to unpack .../libgfortran3_5.2.1-23+rpi1+b1_armhf.deb ...
Unpacking libgfortran3:armhf (5.2.1-23+rpi1+b1) ...
Selecting previously unselected package libblas3.
Preparing to unpack .../libblas3_1.2.20110419-11_armhf.deb ...
Unpacking libblas3 (1.2.20110419-11) ...
Selecting previously unselected package libhdf5-10:armhf.
Preparing to unpack .../libhdf5-10_1.8.15-patch1+docs-5_armhf.deb ...
Unpacking libhdf5-10:armhf (1.8.15-patch1+docs-5) ...
Selecting previously unselected package libhts1:armhf.
Preparing to unpack .../libhts1_1.2.1-1+rpi1_armhf.deb ...
Unpacking libhts1:armhf (1.2.1-1+rpi1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../libjs-jquery_1.11.3+dfsg-4_all.deb ...
Unpacking libjs-jquery (1.11.3+dfsg-4) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../libjs-underscore_1.7.0~dfsg-1_all.deb ...
Unpacking libjs-underscore (1.7.0~dfsg-1) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../libjs-sphinxdoc_1.3.1-8_all.deb ...
Unpacking libjs-sphinxdoc (1.3.1-8) ...
Selecting previously unselected package liblapack3.
Preparing to unpack .../liblapack3_3.5.0-5_armhf.deb ...
Unpacking liblapack3 (3.5.0-5) ...
Selecting previously unselected package python-babel-localedata.
Preparing to unpack .../python-babel-localedata_1.3+dfsg.1-6_all.deb ...
Unpacking python-babel-localedata (1.3+dfsg.1-6) ...
Selecting previously unselected package python-pkg-resources.
Preparing to unpack .../python-pkg-resources_18.4-2_all.deb ...
Unpacking python-pkg-resources (18.4-2) ...
Selecting previously unselected package python-six.
Preparing to unpack .../python-six_1.10.0-1_all.deb ...
Unpacking python-six (1.10.0-1) ...
Selecting previously unselected package python-tz.
Preparing to unpack .../python-tz_2012c+dfsg-0.1_all.deb ...
Unpacking python-tz (2012c+dfsg-0.1) ...
Selecting previously unselected package python-babel.
Preparing to unpack .../python-babel_1.3+dfsg.1-6_all.deb ...
Unpacking python-babel (1.3+dfsg.1-6) ...
Selecting previously unselected package python-cram.
Preparing to unpack .../python-cram_0.6-1_all.deb ...
Unpacking python-cram (0.6-1) ...
Selecting previously unselected package python-roman.
Preparing to unpack .../python-roman_2.0.0-2_all.deb ...
Unpacking python-roman (2.0.0-2) ...
Selecting previously unselected package python-docutils.
Preparing to unpack .../python-docutils_0.12+dfsg-1_all.deb ...
Unpacking python-docutils (0.12+dfsg-1) ...
Selecting previously unselected package python-numpy.
Preparing to unpack .../python-numpy_1%3a1.9.2-5_armhf.deb ...
Unpacking python-numpy (1:1.9.2-5) ...
Selecting previously unselected package python-h5py.
Preparing to unpack .../python-h5py_2.5.0-1+b1_armhf.deb ...
Unpacking python-h5py (2.5.0-1+b1) ...
Selecting previously unselected package python-markupsafe.
Preparing to unpack .../python-markupsafe_0.23-2_armhf.deb ...
Unpacking python-markupsafe (0.23-2) ...
Selecting previously unselected package python-jinja2.
Preparing to unpack .../python-jinja2_2.8-1_all.deb ...
Unpacking python-jinja2 (2.8-1) ...
Selecting previously unselected package python-nose.
Preparing to unpack .../python-nose_1.3.6-1_all.deb ...
Unpacking python-nose (1.3.6-1) ...
Selecting previously unselected package python-pysam.
Preparing to unpack .../python-pysam_0.8.4+ds-1_armhf.deb ...
Unpacking python-pysam (0.8.4+ds-1) ...
Selecting previously unselected package python-pbcore.
Preparing to unpack .../python-pbcore_1.2.6+dfsg-1_all.deb ...
Unpacking python-pbcore (1.2.6+dfsg-1) ...
Selecting previously unselected package python-pygments.
Preparing to unpack .../python-pygments_2.0.1+dfsg-1.1_all.deb ...
Unpacking python-pygments (2.0.1+dfsg-1.1) ...
Selecting previously unselected package python-setuptools.
Preparing to unpack .../python-setuptools_18.4-2_all.deb ...
Unpacking python-setuptools (18.4-2) ...
Selecting previously unselected package python-alabaster.
Preparing to unpack .../python-alabaster_0.7.6-1_all.deb ...
Unpacking python-alabaster (0.7.6-1) ...
Selecting previously unselected package libjs-modernizr.
Preparing to unpack .../libjs-modernizr_2.6.2+ds1-1_all.deb ...
Unpacking libjs-modernizr (2.6.2+ds1-1) ...
Selecting previously unselected package sphinx-rtd-theme-common.
Preparing to unpack .../sphinx-rtd-theme-common_0.1.9-1_all.deb ...
Unpacking sphinx-rtd-theme-common (0.1.9-1) ...
Selecting previously unselected package python-sphinx-rtd-theme.
Preparing to unpack .../python-sphinx-rtd-theme_0.1.9-1_all.deb ...
Unpacking python-sphinx-rtd-theme (0.1.9-1) ...
Selecting previously unselected package sphinx-common.
Preparing to unpack .../sphinx-common_1.3.1-8_all.deb ...
Unpacking sphinx-common (1.3.1-8) ...
Selecting previously unselected package python-sphinx.
Preparing to unpack .../python-sphinx_1.3.1-8_all.deb ...
Unpacking python-sphinx (1.3.1-8) ...
Selecting previously unselected package sbuild-build-depends-python-pbh5tools-dummy.
Preparing to unpack .../sbuild-build-depends-python-pbh5tools-dummy.deb ...
Unpacking sbuild-build-depends-python-pbh5tools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-22) ...
Setting up libgomp1:armhf (5.2.1-23+rpi1+b1) ...
Setting up libatomic1:armhf (5.2.1-23+rpi1+b1) ...
Setting up libasan2:armhf (5.2.1-23+rpi1+b1) ...
Setting up libubsan0:armhf (5.2.1-23+rpi1+b1) ...
Setting up libisl15:armhf (0.15-3) ...
Setting up cpp-5 (5.2.1-23+rpi1+b1) ...
Setting up libcc1-0:armhf (5.2.1-23+rpi1+b1) ...
Setting up libgcc-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up gcc-5 (5.2.1-23+rpi1+b1) ...
Setting up libstdc++-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up g++-5 (5.2.1-23+rpi1+b1) ...
Setting up groff-base (1.22.3-4) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libffi6:armhf (3.2.1-3) ...
Setting up libsqlite3-0:armhf (3.9.2-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.10-5+b1) ...
Setting up python2.7 (2.7.10-5+b1) ...
Setting up libpython-stdlib:armhf (2.7.9-1) ...
Setting up python (2.7.9-1) ...
Setting up fonts-lato (2.0-1) ...
Setting up libmpdec2:armhf (2.4.1-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libpython3.4-stdlib:armhf (3.4.3-10+b1) ...
Setting up python3.4 (3.4.3-10+b1) ...
Setting up libpython3-stdlib:armhf (3.4.3-7) ...
Setting up sgml-base (1.26+nmu4) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libicu55:armhf (55.1-6) ...
Setting up libxml2:armhf (2.9.2+zdfsg1-4) ...
Setting up libglib2.0-0:armhf (2.46.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.9-1) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up xml-core (0.13+nmu2) ...
Setting up fonts-font-awesome (4.4.0~dfsg-1) ...
Setting up libblas-common (1.2.20110419-11) ...
Setting up libgfortran3:armhf (5.2.1-23+rpi1+b1) ...
Setting up libblas3 (1.2.20110419-11) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libhdf5-10:armhf (1.8.15-patch1+docs-5) ...
Setting up libhts1:armhf (1.2.1-1+rpi1) ...
Setting up libjs-jquery (1.11.3+dfsg-4) ...
Setting up libjs-underscore (1.7.0~dfsg-1) ...
Setting up libjs-sphinxdoc (1.3.1-8) ...
Setting up liblapack3 (3.5.0-5) ...
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-babel-localedata (1.3+dfsg.1-6) ...
Setting up python-pkg-resources (18.4-2) ...
Setting up python-six (1.10.0-1) ...
Setting up python-tz (2012c+dfsg-0.1) ...
Setting up python-babel (1.3+dfsg.1-6) ...
update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python-cram (0.6-1) ...
Setting up python-roman (2.0.0-2) ...
Setting up python-numpy (1:1.9.2-5) ...
Setting up python-h5py (2.5.0-1+b1) ...
Setting up python-markupsafe (0.23-2) ...
Setting up python-jinja2 (2.8-1) ...
Setting up python-nose (1.3.6-1) ...
Setting up python-pysam (0.8.4+ds-1) ...
Setting up python-pbcore (1.2.6+dfsg-1) ...
Setting up python-pygments (2.0.1+dfsg-1.1) ...
Setting up python-setuptools (18.4-2) ...
Setting up libjs-modernizr (2.6.2+ds1-1) ...
Setting up sphinx-rtd-theme-common (0.1.9-1) ...
Setting up python-sphinx-rtd-theme (0.1.9-1) ...
Setting up sphinx-common (1.3.1-8) ...
Processing triggers for sgml-base (1.26+nmu4) ...
Setting up docutils-common (0.12+dfsg-1) ...
Processing triggers for sgml-base (1.26+nmu4) ...
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 python-alabaster (0.7.6-1) ...
Setting up python-sphinx (1.3.1-8) ...
Setting up dh-python (2.20151103) ...
Setting up python3 (3.4.3-7) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Setting up debhelper (9.20151005) ...
Setting up sbuild-build-depends-python-pbh5tools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-22) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-5_5.2.1-23+rpi1+b1 gcc-5_5.2.1-23+rpi1+b1 libc6-dev_2.19-22 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-5_5.2.1-23+rpi1+b1 dash_0.5.7-4 debconf_1.5.58 debconf-i18n_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-python_2.20151103 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 docutils-common_0.12+dfsg-1 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 fonts-font-awesome_4.4.0~dfsg-1 fonts-lato_2.0-1 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-23+rpi1+b1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1+b1 gcc-5-base_5.2.1-23+rpi1+b1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan2_5.2.1-23+rpi1+b1 libatomic1_5.2.1-23+rpi1+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblas-common_1.2.20110419-11 libblas3_1.2.20110419-11 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1+b1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1 libdebconfclient0_0.197 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7 libgcc-5-dev_5.2.1-23+rpi1+b1 libgcc1_1:5.2.1-23+rpi1+b1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libgfortran3_5.2.1-23+rpi1+b1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.2.1-23+rpi1+b1 libgpg-error0_1.20-1 libhdf5-10_1.8.15-patch1+docs-5 libhts1_1.2.1-1+rpi1 libicu55_55.1-6 libisl13_0.14-2 libisl15_0.15-3 libjs-jquery_1.11.3+dfsg-4 libjs-modernizr_2.6.2+ds1-1 libjs-sphinxdoc_1.3.1-8 libjs-underscore_1.7.0~dfsg-1 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblapack3_3.5.0-5 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpdec2_2.4.1-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libplymouth4_0.9.2-3 libpng12-0_1.2.54-1 libprocps4_2:3.3.10-2 libpython-stdlib_2.7.9-1 libpython2.7-minimal_2.7.10-5+b1 libpython2.7-stdlib_2.7.10-5+b1 libpython3-stdlib_3.4.3-7 libpython3.4-minimal_3.4.3-10+b1 libpython3.4-stdlib_3.4.3-10+b1 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 libsmartcols1_2.27.1-1 libsqlite3-0_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2d-3 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.2.1-23+rpi1+b1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 mountall_2.54 multiarch-support_2.19-22 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 plymouth_0.9.2-3 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 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_2.5.0-1+b1 python-jinja2_2.8-1 python-markupsafe_0.23-2 python-minimal_2.7.9-1 python-nose_1.3.6-1 python-numpy_1:1.9.2-5 python-pbcore_1.2.6+dfsg-1 python-pkg-resources_18.4-2 python-pygments_2.0.1+dfsg-1.1 python-pysam_0.8.4+ds-1 python-roman_2.0.0-2 python-setuptools_18.4-2 python-six_1.10.0-1 python-sphinx_1.3.1-8 python-sphinx-rtd-theme_0.1.9-1 python-tz_2012c+dfsg-0.1 python2.7_2.7.10-5+b1 python2.7-minimal_2.7.10-5+b1 python3_3.4.3-7 python3-minimal_3.4.3-7 python3.4_3.4.3-10+b1 python3.4-minimal_3.4.3-10+b1 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_1.3.1-8 sphinx-rtd-theme-common_0.1.9-1 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_228-2 util-linux_2.27.1-1 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 Nov 29 06:39:43 2015 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./python-pbh5tools_0.8.0+dfsg-3.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-3.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
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=root
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-5d46c282-3796-433a-80ed-b2cb0486e5d8
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package python-pbh5tools
dpkg-buildpackage: source version 0.8.0+dfsg-3
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_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 -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 -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -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 v1.3.1
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
WARNING: html_static_path entry u'/«BUILDDIR»/python-pbh5tools-0.8.0+dfsg/doc/_static' does not exist
copying static files... 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.
make[2]: [examples] Error 1 (ignored)
Makefile:26: recipe for target 'examples' failed
sed 's/^ / /' doc/examples.t > doc/examples.md
find tests -name "*.py" | xargs nosetests -v
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
test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Merge) ... ok
test_basic (test_cmph5lib_CmpH5Merge.TestCmpH5Select) ... ok
test_output_file_in_inputs (test_cmph5lib_CmpH5Merge.TestMergeException) ... ok
----------------------------------------------------------------------
Ran 10 tests in 47.187s
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.
make[2]: [test] Error 123 (ignored)
Makefile:20: recipe for target 'test' failed
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
mv /«BUILDDIR»/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin/bash5tools.py /«BUILDDIR»/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin/bash5tools
mv /«BUILDDIR»/python-pbh5tools-0.8.0+dfsg/debian/python-pbh5tools/usr/bin/cmph5tools.py /«BUILDDIR»/python-pbh5tools-0.8.0+dfsg/debian/python-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_installman -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}
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-pbh5tools' in '../python-pbh5tools_0.8.0+dfsg-3_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pbh5tools_0.8.0+dfsg-3_armhf.changes
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 20151204-1148
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
python-pbh5tools_0.8.0+dfsg-3_armhf.changes:
────────────────────────────────────────────
Format: 1.8
Date: Sat, 28 Nov 2015 21:51:12 -0800
Source: python-pbh5tools
Binary: python-pbh5tools python-pbh5tools-doc
Architecture: armhf
Version: 0.8.0+dfsg-3
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@ghraoui.name>
Description:
python-pbh5tools - tools for manipulating HDF5 files produced by Pacific Biosciences
python-pbh5tools-doc - tools for manipulating HDF5 files produced by Pacific Biosciences
Changes:
python-pbh5tools (0.8.0+dfsg-3) unstable; urgency=low
.
* Don't install LICENSES.txt file
* Ignore cram test results because of spurious failures
Checksums-Sha1:
84a5371a87a45ffc238c98eac15d74c242515b8b 32722 python-pbh5tools_0.8.0+dfsg-3_armhf.deb
Checksums-Sha256:
14ff7eb110c6ce32f3fb7cc70b6efc72593bd9c51fa45016e77f166141bd9515 32722 python-pbh5tools_0.8.0+dfsg-3_armhf.deb
Files:
71cc4b377fd2f2950b555c98f6ebb422 32722 python optional python-pbh5tools_0.8.0+dfsg-3_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
python-pbh5tools_0.8.0+dfsg-3_armhf.deb
───────────────────────────────────────
new debian package, version 2.0.
size 32722 bytes: control archive=1717 bytes.
793 bytes, 16 lines control
2445 bytes, 28 lines md5sums
164 bytes, 9 lines * postinst #!/bin/sh
267 bytes, 14 lines * prerm #!/bin/sh
Package: python-pbh5tools
Version: 0.8.0+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 163
Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcore, python:any (>= 2.7.5-5~), python-pkg-resources
Section: python
Priority: optional
Homepage: https://github.com/PacificBiosciences/pbh5tools
Description: tools for manipulating HDF5 files produced by Pacific Biosciences
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.
.
This package is part of the SMRTAnalysis suite.
drwxr-xr-x root/root 0 2015-12-04 11:48 ./
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/bin/
-rwxr-xr-x root/root 6895 2015-12-04 11:41 ./usr/bin/bash5tools
lrwxrwxrwx root/root 0 2015-12-04 11:48 ./usr/bin/bash5tools.py -> bash5tools
-rwxr-xr-x root/root 12055 2015-12-04 11:41 ./usr/bin/cmph5tools
lrwxrwxrwx root/root 0 2015-12-04 11:48 ./usr/bin/cmph5tools.py -> cmph5tools
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/lib/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/
-rw-r--r-- root/root 1827 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/dependency_links.txt
-rw-r--r-- root/root 1 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/not-zip-safe
-rw-r--r-- root/root 0 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/requires.txt
-rw-r--r-- root/root 23 2015-12-04 11:48 ./usr/lib/python2.7/dist-packages/pbh5tools-0.8.0.egg-info/top_level.txt
drwxr-xr-x root/root 0 2015-12-04 11:48 ./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 5364 2015-12-04 11:48 ./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 2015-12-04 11:48 ./usr/share/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/share/doc/python-pbh5tools/
-rw-r--r-- root/root 253 2015-08-15 19:12 ./usr/share/doc/python-pbh5tools/README.md
-rw-r--r-- root/root 500 2015-11-29 05:52 ./usr/share/doc/python-pbh5tools/changelog.Debian.gz
-rw-r--r-- root/root 1977 2015-11-15 11:46 ./usr/share/doc/python-pbh5tools/copyright
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/share/doc/python-pbh5tools/examples/
-rw-r--r-- root/root 3058 2015-12-04 11:44 ./usr/share/doc/python-pbh5tools/examples/examples.md.gz
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/share/man/
drwxr-xr-x root/root 0 2015-12-04 11:48 ./usr/share/man/man1/
-rw-r--r-- root/root 695 2015-12-04 11:48 ./usr/share/man/man1/bash5tools.1.gz
lrwxrwxrwx root/root 0 2015-12-04 11:48 ./usr/share/man/man1/bash5tools.py.1.gz -> bash5tools.1.gz
-rw-r--r-- root/root 655 2015-12-04 11:48 ./usr/share/man/man1/cmph5tools.1.gz
lrwxrwxrwx root/root 0 2015-12-04 11:48 ./usr/share/man/man1/cmph5tools.py.1.gz -> cmph5tools.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 11396
Build-Time: 483
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 560
Job: python-pbh5tools_0.8.0+dfsg-3
Machine Architecture: armhf
Package: python-pbh5tools
Package-Time: 1117
Source-Version: 0.8.0+dfsg-3
Space: 11396
Status: successful
Version: 0.8.0+dfsg-3
────────────────────────────────────────────────────────────────────────────────
Finished at 20151204-1148
Build needed 00:18:37, 11396k disc space