kineticstools →
0.6.1+20161222-1 →
armhf → 2017-01-26 08:14:15
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| kineticstools 0.6.1+20161222-1 (armhf) Thu, 26 Jan 2017 06:44:52 +0000 |
+==============================================================================+
Package: kineticstools
Version: 0.6.1+20161222-1
Source Version: 0.6.1+20161222-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-1e7597a6-3c25-4ee7-b44e-8fb9e8f90d78' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9731 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 26s (811 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'kineticstools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/kineticstools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/kineticstools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 114 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main kineticstools 0.6.1+20161222-1 (dsc) [2427 B]
Get:2 http://172.17.0.1/private stretch-staging/main kineticstools 0.6.1+20161222-1 (tar) [114 MB]
Get:3 http://172.17.0.1/private stretch-staging/main kineticstools 0.6.1+20161222-1 (diff) [7424 B]
Fetched 114 MB in 34s (3334 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/kineticstools-T81Dl0/kineticstools-0.6.1+20161222' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/kineticstools-T81Dl0' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-LBaFm0/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-LBaFm0/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-LBaFm0/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3435 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 63 not upgraded.
Need to get 774 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 774 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13244 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose
Filtered Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python-docutils, python-pbcore (>= 1.2.8), python-pbcommand (>= 0.3.22), python-numpy (>= 1.6.0), python-h5py (>= 1.3.0), python-scipy (>= 0.9.0), python-nose
dpkg-deb: building package 'sbuild-build-depends-kineticstools-dummy' in '/<<BUILDDIR>>/resolver-LBaFm0/apt_archive/sbuild-build-depends-kineticstools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-kineticstools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Sources [571 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ Packages [653 B]
Fetched 2557 B in 0s (3716 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install kineticstools build dependencies (apt-based resolver)
-------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n kbd libfuse2 manpages netbase psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
file gettext gettext-base groff-base intltool-debian libaec0
libarchive-zip-perl libblas-common libblas3 libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhdf5-100
libhogweed4 libhts1 libicu57 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc
libmagic1 libmpdec2 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1
libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib librtmp1
libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsz2
libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support openssl po-debconf python python-all python-avro python-chardet
python-decorator python-docutils python-h5py python-iso8601 python-minimal
python-nose python-numpy python-pbcommand python-pbcore python-pkg-resources
python-pysam python-requests python-roman python-scipy python-setuptools
python-six python-urllib3 python2.7 python2.7-minimal python3
python3-minimal python3.5 python3.5-minimal sgml-base xml-core
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
gnutls-bin krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk
fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
texlive-latex-base texlive-latex-recommended python-h5py-doc python-coverage
python-nose-doc gfortran python-dev python-numpy-dbg python-numpy-doc
python-pbcore-doc python-cryptography python-idna python-openssl
python-socks python-scipy-doc python-setuptools-doc python-ntlm
python2.7-doc binfmt-support python3-doc python3-tk python3-venv
python3.5-venv python3.5-doc sgml-base-doc
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl
docutils-doc libpaper-utils python-pil python-pygments python-dev
python-imaging python-cryptography python-idna python-ipaddress
python-openssl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
debhelper dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
file gettext gettext-base groff-base intltool-debian libaec0
libarchive-zip-perl libblas-common libblas3 libbsd0 libcroco3
libcurl3-gnutls libexpat1 libffi6 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhdf5-100
libhogweed4 libhts1 libicu57 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc
libmagic1 libmpdec2 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1
libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib
libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib librtmp1
libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libsz2
libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support openssl po-debconf python python-all python-avro python-chardet
python-decorator python-docutils python-h5py python-iso8601 python-minimal
python-nose python-numpy python-pbcommand python-pbcore python-pkg-resources
python-pysam python-requests python-roman python-scipy python-setuptools
python-six python-urllib3 python2.7 python2.7-minimal python3
python3-minimal python3.5 python3.5-minimal
sbuild-build-depends-kineticstools-dummy sgml-base xml-core
0 upgraded, 103 newly installed, 0 to remove and 63 not upgraded.
Need to get 57.3 MB/57.7 MB of archives.
After this operation, 202 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-LBaFm0/apt_archive ./ sbuild-build-depends-kineticstools-dummy 0.invalid.0 [856 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.13-1 [389 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.13-1 [1180 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.13-1 [40.5 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-2 [62.2 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0c-2 [1101 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.13-1 [1828 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.13-1 [285 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.13-1 [19.9 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.13-1 [154 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.3~rc1-1 [566 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.3~rc1-1 [1439 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-4 [35.3 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.3~rc1-1 [2091 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.3~rc1-1 [229 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-4 [18.6 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20160818 [83.0 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-4 [21.7 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf sgml-base all 1.29 [14.8 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-2 [221 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-2 [104 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-2 [63.1 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.8-1 [823 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-2 [66.8 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-2 [98.0 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-3 [84.5 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-3 [194 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.1.0c-2 [703 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20161130 [203 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 13 [15.8 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.029-2 [15.3 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.029-2 [9330 B]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.3 [829 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf xml-core all 0.17 [23.2 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf docutils-common all 0.13.1+dfsg-1 [199 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.7.0-1 [14.0 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.1-5+rpi1 [166 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.7.0-1 [107 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libidn2-0 armhf 0.14-1 [58.3 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.17.0-1 [70.1 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libpsl5 armhf 0.16.1-1 [41.2 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.52.1-1 [258 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-1+rpi1 [215 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.7.0-1 [1503 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf python-all armhf 2.7.13-1 [940 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf python-avro all 1.8.1+dfsg-1 [58.1 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf python-pkg-resources all 32.3.1-1 [166 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf python-chardet all 2.3.0-2 [96.0 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf python-decorator all 4.0.10-1 [13.2 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf python-roman all 2.0.0-2 [8130 B]
Get:87 http://172.17.0.1/private stretch-staging/main armhf python-docutils all 0.13.1+dfsg-1 [373 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf python-numpy armhf 1:1.12.0~rc2-1 [1693 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf python-six all 1.10.0-3 [14.4 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf python-h5py armhf 2.6.0-2 [469 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf python-nose all 1.3.7-2 [132 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf python-iso8601 all 0.1.11-1 [12.7 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf python-urllib3 all 1.19.1-1 [77.5 kB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf python-requests all 2.12.4-1 [101 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf python-pbcommand all 0.5.3-1 [79.6 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf python-pysam armhf 0.9.1.4+ds-1+rpi1 [985 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf python-pbcore all 1.2.10+dfsg-1 [9083 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf python-setuptools all 32.3.1-1 [301 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf python-scipy armhf 0.18.1-2 [8094 kB]
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173 added, 0 removed; done.
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Setting up autopoint (0.19.8.1-1) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up libfile-stripnondeterminism-perl (0.029-2) ...
Setting up libidn2-0:armhf (0.14-1) ...
Setting up libhdf5-100:armhf (1.10.0-patch1+docs-3) ...
Setting up libpsl5:armhf (0.16.1-1) ...
Setting up liblapack3 (3.7.0-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up libpython3.5-stdlib:armhf (3.5.3~rc1-1) ...
Setting up python2.7 (2.7.13-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-2) ...
Setting up libkrb5support0:armhf (1.15-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libpython-stdlib:armhf (2.7.13-1) ...
Setting up libp11-kit0:armhf (0.23.3-2) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.13-1) ...
Setting up libtool (2.4.6-2) ...
Setting up python3.5 (3.5.3~rc1-1) ...
Setting up libpython3-stdlib:armhf (3.5.1-4) ...
Setting up libk5crypto3:armhf (1.15-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libgnutls30:armhf (3.5.8-1) ...
Setting up python-avro (1.8.1+dfsg-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up python-pkg-resources (32.3.1-1) ...
Setting up python-roman (2.0.0-2) ...
Setting up python-numpy (1:1.12.0~rc2-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up python-six (1.10.0-3) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-3) ...
Setting up python-iso8601 (0.1.11-1) ...
Setting up libkrb5-3:armhf (1.15-1) ...
Setting up python-decorator (4.0.10-1) ...
Setting up python-nose (1.3.7-2) ...
Setting up python-all (2.7.13-1) ...
Setting up python-setuptools (32.3.1-1) ...
Setting up python-urllib3 (1.19.1-1) ...
Setting up python-h5py (2.6.0-2) ...
Setting up python-chardet (2.3.0-2) ...
Setting up python-scipy (0.18.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libgssapi-krb5-2:armhf (1.15-1) ...
Setting up python-requests (2.12.4-1) ...
Setting up python-pbcommand (0.5.3-1) ...
Setting up libcurl3-gnutls:armhf (7.52.1-1) ...
Setting up libhts1:armhf (1.3.2-1+rpi1) ...
Setting up python-pysam (0.9.1.4+ds-1+rpi1) ...
Setting up python-pbcore (1.2.10+dfsg-1) ...
Processing triggers for sgml-base (1.29) ...
Setting up docutils-common (0.13.1+dfsg-1) ...
Processing triggers for sgml-base (1.29) ...
Setting up python-docutils (0.13.1+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/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up dh-autoreconf (13) ...
Setting up python3 (3.5.1-4) ...
Setting up dh-python (2.20160818) ...
Setting up debhelper (10.2.3) ...
Setting up sbuild-build-depends-kineticstools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.029-2) ...
Processing triggers for libc-bin (2.24-7+rpi1) ...
Processing triggers for ca-certificates (20161130) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.1-5+rpi1 gcc-6_6.2.1-5+rpi1 libc6-dev_2.24-7+rpi1 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4~beta1 autoconf_2.69-10 automake_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.7+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20161130 coreutils_8.25-2 cpio_2.11+dfsg-6 cpp_4:6.1.1-1 cpp-6_6.2.1-5+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.3 debianutils_4.8.1 dh-autoreconf_13 dh-python_2.20160818 dh-strip-nondeterminism_0.029-2 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 docutils-common_0.13.1+dfsg-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-2 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.1-5+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.1-5+rpi1 gcc-6-base_6.2.1-5+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libaec0_0.3.2-1 libapparmor1_2.10.95-6 libapt-pkg5.0_1.4~beta1 libarchive-zip-perl_1.59-1 libasan3_6.2.1-5+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.1-5+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.7.0-1 libblas3_3.7.0-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-7+rpi1 libc-dev-bin_2.24-7+rpi1 libc6_2.24-7+rpi1 libc6-dev_2.24-7+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.1-5+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 libcurl3-gnutls_7.52.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.14-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.74-1 libexpat1_2.2.0-2 libfakeroot_1.21-2 libfdisk1_2.29-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.029-2 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.1-5+rpi1 libgcc1_1:6.2.1-5+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.1-5+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.8-1 libgomp1_6.2.1-5+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15-1 libhdf5-100_1.10.0-patch1+docs-3 libhogweed4_3.3-1 libhts1_1.3.2-1+rpi1 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.14-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 liblapack3_3.7.0-1 libldap-2.4-2_2.4.44+dfsg-3 libldap-common_2.4.44+dfsg-3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-2 libmagic1_1:5.29-2 libmount1_2.29-1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.17.0-1 libnpth0_1.3-1 libp11-kit0_0.23.3-2 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc4-1 libpipeline1_1.4.1-2 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libpsl5_0.16.1-1 libpython-stdlib_2.7.13-1 libpython2.7-minimal_2.7.13-1 libpython2.7-stdlib_2.7.13-1 libpython3-stdlib_3.5.1-4 libpython3.5-minimal_3.5.3~rc1-1 libpython3.5-stdlib_3.5.3~rc1-1 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.1_1.1.0c-2 libstdc++-6-dev_6.2.1-5+rpi1 libstdc++6_6.2.1-5+rpi1 libsystemd0_232-6 libsz2_0.3.2-1 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.1-5+rpi1 libudev1_232-6 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.3 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.08-1 mawk_1.3.3-17 mime-support_3.60 mount_2.29-1 multiarch-support_2.24-7+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 openssl_1.1.0c-2 passwd_1:4.2-3.3 patch_2.7.5-1 perl_5.24.1~rc4-1 perl-base_5.24.1~rc4-1 perl-modules-5.24_5.24.1~rc4-1 pinentry-curses_0.9.7-9 po-debconf_1.0.20 procps_2:3.3.12-3 psmisc_22.21-2.1 python_2.7.13-1 python-all_2.7.13-1 python-avro_1.8.1+dfsg-1 python-chardet_2.3.0-2 python-decorator_4.0.10-1 python-docutils_0.13.1+dfsg-1 python-h5py_2.6.0-2 python-iso8601_0.1.11-1 python-minimal_2.7.13-1 python-nose_1.3.7-2 python-numpy_1:1.12.0~rc2-1 python-pbcommand_0.5.3-1 python-pbcore_1.2.10+dfsg-1 python-pkg-resources_32.3.1-1 python-pysam_0.9.1.4+ds-1+rpi1 python-requests_2.12.4-1 python-roman_2.0.0-2 python-scipy_0.18.1-2 python-setuptools_32.3.1-1 python-six_1.10.0-3 python-urllib3_1.19.1-1 python2.7_2.7.13-1 python2.7-minimal_2.7.13-1 python3_3.5.1-4 python3-minimal_3.5.1-4 python3.5_3.5.3~rc1-1 python3.5-minimal_3.5.3~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-kineticstools-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 sgml-base_1.29 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016j-2 udev_232-6 util-linux_2.29-1 xml-core_0.17 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Jan 15 23:55:41 2017 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./kineticstools_0.6.1+20161222-1.dsc
dpkg-source: info: extracting kineticstools in /<<BUILDDIR>>/kineticstools-0.6.1+20161222
dpkg-source: info: unpacking kineticstools_0.6.1+20161222.orig.tar.gz
dpkg-source: info: unpacking kineticstools_0.6.1+20161222-1.debian.tar.xz
dpkg-source: info: applying man-pages.patch
dpkg-source: info: applying tests-import.patch
dpkg-source: info: applying verbose-testing.patch
dpkg-source: info: applying deactivate-tests-requiring-unavailable-data.patch
dpkg-source: info: applying compiled-extension.patch
dpkg-source: info: applying spelling.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-1e7597a6-3c25-4ee7-b44e-8fb9e8f90d78
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package kineticstools
dpkg-buildpackage: info: source version 0.6.1+20161222-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build kineticstools-0.6.1+20161222
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2 --buildsystem=pybuild
dh_testdir -O--buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
dh_clean -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch --with python2 --buildsystem=pybuild
dh_testdir -a -O--buildsystem=pybuild
dh_update_autotools_config -a -O--buildsystem=pybuild
dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config
running config
dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build
running build
running build_py
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
copying kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks
copying kineticsTools/tasks/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks
copying kineticsTools/tasks/gather_kinetics_h5.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
copying kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources
running build_ext
building 'kineticsTools/tree_predict' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/kineticsTools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/kineticstools-0.6.1+20161222=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c kineticsTools/tree_predict.c -o build/temp.linux-armv7l-2.7/kineticsTools/tree_predict.o -O3 -shared -std=c99
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-Xzhqjt/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/kineticstools-0.6.1+20161222=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/kineticsTools/tree_predict.o -o /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:184: cd /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose test
Check the null model against a few hard-coded contexts ... ok
Test a modification decode around a known modification in lambda ... ok
runTest (test.TestSetup) ... ok
test_bam (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_cmph5 (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_createReferenceWindows (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_dataset (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_enumerateChunks (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_parseReferenceWindow (test_ReferenceUtils.ReferenceUtilsTest) ... SKIP: Shared data folder missing
test_run_e2e (test_gather_h5.TestGatherH5ToolContract) ... ok
test_gather_kinetics_h5 (test_gather_h5.TestGatherHDF5) ... ok
test_gather_kinetics_h5 (test_gather_h5.TestGatherHDF5Flat) ... ok
test_private_api (test_inputs.TestBam) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_small_decode (test_inputs.TestChunkedDataset) ... SKIP: Missing test data directory
test_private_api (test_inputs.TestDataset) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
test_small_decode (test_inputs.TestNonStochastic) ... SKIP: Missing test data directory
test_private_api (test_inputs.TestSplitDataset) ... SKIP: Missing test data directory
Test for known modifications near the start of H. pylori genome ... SKIP: Missing test data directory
SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestIpdSummary) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
test_run_e2e (test_tool_contract.TestIpdSummaryChunk) ... SKIP: FIXME
test_run_e2e (test_tool_contract.TestSummarizeModifications) ... SKIP: /pbi/dept/secondary/siv/testdata/kineticsTools or /pbi/dept/secondary/siv/references/Helicobacter_pylori_J99 not available
----------------------------------------------------------------------
Ran 23 tests in 615.578s
OK (SKIP=18)
Pos: 3, TplStrand: 0
Got ctx: NGGGCGGCGACCTCG
Lut prediction: 0.692615
Gbm prediction: 0.692615
Gbm prediction fast: 0.692615
Gbm pred via predictIpdFuncModel: 0.692615
Methylated prediction: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction: NGGGCGGCGJCCTCG -> 0.481690
Methylated prediction fast: NGGGJGGCGACCTCG -> 0.809961
Methylated prediction fast: NGGGCGGCGJCCTCG -> 0.481690
Pos: 10, TplStrand: 0
Got ctx: CGACCTCGCGGGTTT
Lut prediction: 0.439837
Gbm prediction: 0.439837
Gbm prediction fast: 0.439837
Gbm pred via predictIpdFuncModel: 0.439837
Methylated prediction: CGACJTCGCGGGTTT -> 1.806269
Methylated prediction: CGACCTCGCJGGTTT -> 0.418073
Methylated prediction fast: CGACJTCGCGGGTTT -> 1.806269
Methylated prediction fast: CGACCTCGCJGGTTT -> 0.418073
Pos: 20, TplStrand: 0
Got ctx: GGTTTTCGCTATTTA
Lut prediction: 0.803713
Gbm prediction: 0.803713
Gbm prediction fast: 0.803713
Gbm pred via predictIpdFuncModel: 0.803713
Pos: 30, TplStrand: 0
Got ctx: ATTTATGAAAATTTT
Lut prediction: 0.497546
Gbm prediction: 0.497546
Gbm prediction fast: 0.497546
Gbm pred via predictIpdFuncModel: 0.497546
Methylated prediction: ATTTHTGAAAATTTT -> 3.467282
Methylated prediction: ATTTATGAAHATTTT -> 0.462962
Methylated prediction fast: ATTTHTGAAAATTTT -> 3.467282
Methylated prediction fast: ATTTATGAAHATTTT -> 0.462962
Pos: 31, TplStrand: 0
Got ctx: TTTATGAAAATTTTC
Lut prediction: 0.425639
Gbm prediction: 0.425639
Gbm prediction fast: 0.425639
Gbm pred via predictIpdFuncModel: 0.425639
Pos: 32, TplStrand: 0
Got ctx: TTATGAAAATTTTCC
Lut prediction: 0.387926
Gbm prediction: 0.387926
Gbm prediction fast: 0.387926
Gbm pred via predictIpdFuncModel: 0.387926
Pos: 33, TplStrand: 0
Got ctx: TATGAAAATTTTCCG
Lut prediction: 1.008767
Gbm prediction: 1.008767
Gbm prediction fast: 1.008767
Gbm pred via predictIpdFuncModel: 1.008767
Methylated prediction: TATGHAAATTTTCCG -> 6.857647
Methylated prediction: TATGAAAATHTTCCG -> 1.047730
Methylated prediction fast: TATGHAAATTTTCCG -> 6.857647
Methylated prediction fast: TATGAAAATHTTCCG -> 1.047730
Pos: 34, TplStrand: 0
Got ctx: ATGAAAATTTTCCGG
Lut prediction: 1.700875
Gbm prediction: 1.700875
Gbm prediction fast: 1.700875
Gbm pred via predictIpdFuncModel: 1.700875
Methylated prediction: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction: ATGAAAATTHTCCGG -> 2.211950
Methylated prediction fast: ATGAHAATTTTCCGG -> 9.737025
Methylated prediction fast: ATGAAAATTHTCCGG -> 2.211950
[{'LLR': 44.9363980691445, 'tpl': 14982, 'Mask': [-5, 0], 'modification': 'm6A', 'strand': 0, 'QMod': 195.15629718037397}, {'LLR': 0.7833812384793148, 'tpl': 15040, 'Mask': [-1, 3], 'modification': 'm6A', 'strand': 1, 'QMod': 5.0363556562304366}, {'LLR': 45.588426682175815, 'tpl': 14991, 'Mask': [-5, 0, 1], 'modification': 'm6A', 'strand': 1, 'QMod': 197.98802146719927}, {'LLR': 12.04025630132049, 'tpl': 14997, 'Mask': [-8, -5, 1, 2, 3], 'modification': 'm4C', 'strand': 1, 'QMod': 52.290194354679265}, {'LLR': 5.787841909938088, 'tpl': 14996, 'Mask': [-6, -3, 1, 2], 'modification': 'm4C', 'strand': 1, 'QMod': 25.14956702352173}]
fakeroot debian/rules binary-arch
dh binary-arch --with python2 --buildsystem=pybuild
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/kineticstools-0.6.1+20161222'
dh_auto_install
I: pybuild base:184: /usr/bin/python setup.py install --root /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools
running install
running build
running build_py
running build_ext
running install_lib
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ResultWriter.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdSummary.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/pipelineTools.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/summarizeModifications.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/__init__.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/gather_kinetics_h5.py -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tasks/gather_kinetics_h5.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks
creating /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P4-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P5-C3.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/P6-C4.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-C2.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/XL-XL.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/resources/unknown.h5 -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/tree_predict.so -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/__init__.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/KineticWorker.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MixtureEstimationMethods.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteCommon.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MultiSiteDetection.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/MedakaLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/BasicLdaEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/PositiveControlEnricher.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ModificationDecode.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/WorkerProcess.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ipdModel.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/sharedArray.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ReferenceUtils.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/ResultWriter.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
copying /<<BUILDDIR>>/kineticstools-0.6.1+20161222/.pybuild/pythonX.Y_2.7/build/kineticsTools/pipelineTools.pyc -> /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py to BasicLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py to KineticWorker.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py to MedakaLdaEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py to MixtureEstimationMethods.pyc
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byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py to MultiSiteDetection.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py to PositiveControlEnricher.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py to ReferenceUtils.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py to ResultWriter.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py to WorkerProcess.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py to ipdSummary.pyc
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byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py to summarizeModifications.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py to ipdModel.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py to gather_kinetics_h5.pyc
running install_egg_info
running egg_info
creating kineticsTools.egg-info
writing requirements to kineticsTools.egg-info/requires.txt
writing kineticsTools.egg-info/PKG-INFO
writing top-level names to kineticsTools.egg-info/top_level.txt
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writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
reading manifest file 'kineticsTools.egg-info/SOURCES.txt'
writing manifest file 'kineticsTools.egg-info/SOURCES.txt'
Copying kineticsTools.egg-info to /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info
Skipping SOURCES.txt
running install_scripts
Installing ipdSummary script to /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/bin
Installing summarizeModifications script to /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/python-kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/bin
mv debian/python-kineticstools/usr/bin/* /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/bin
mkdir -p /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/share/man//man1
rst2man doc/manual.rst > /<<BUILDDIR>>/kineticstools-0.6.1+20161222/debian/kineticstools/usr/share/man//man1/ipdSummary.1
doc/manual.rst:114: (ERROR/3) Malformed table.
Text in column margin in table line 2.
================ ===========
Column Description
================ ===========
seqid Fasta contig name
source Name of tool -- 'kinModCall'
type Modification type -- in identification mode this will be m6A, m4C, or m5C for identified bases, or the generic tag 'modified_base' if a kinetic event was detected that does not match a known modification signature
start Modification position on contig
end Modification position on contig
score Phred transformed p-value of detection - this is the single-site detection p-value
strand Sample strand containing modification
phase Not applicable
attributes Extra fields relevant to base mods. IPDRatio is traditional IPDRatio, context is the reference sequence -20bp to +20bp around the modification, and coverage level is the number of IPD observations used after Mapping QV filtering and accuracy filtering. If the row results from an identified modification we also include an identificationQv tag with the from the modification identification procedure. identificationQv is the phred-transformed probability of an incorrect identification, for bases that were identified as having a particular modification. frac, fracLow, fracUp are the estimated fraction of molecules carrying the modification, and the 5% confidence intervals of the estimate. The methylated fraction estimation is a beta-level feature, and should only be used for exploratory purposes.
================ ===========
doc/manual.rst:46: (WARNING/2) "math" role not supported
doc/manual.rst:48: (WARNING/2) "math" role not supported
doc/manual.rst:48: (WARNING/2) "math" role not supported
mkdir -p debian/kineticstools-data/usr/share/kineticstools
mv debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/
make[1]: Leaving directory '/<<BUILDDIR>>/kineticstools-0.6.1+20161222'
dh_installdocs -a -O--buildsystem=pybuild
dh_installchangelogs -a -O--buildsystem=pybuild
dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:322: renaming tree_predict.so to tree_predict.arm-linux-gnueabihf.so
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
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dh_fixperms -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-kineticstools/usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.arm-linux-gnueabihf.so was not linked against libpthread.so.0 (it uses none of the library's symbols)
dh_installdeb -a -O--buildsystem=pybuild
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dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Versions}
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dpkg-gencontrol: warning: package python-kineticstools: unused substitution variable ${python:Versions}
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-kineticstools-dbgsym' in '../python-kineticstools-dbgsym_0.6.1+20161222-1_armhf.deb'.
dpkg-deb: building package 'python-kineticstools' in '../python-kineticstools_0.6.1+20161222-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../kineticstools_0.6.1+20161222-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build kineticstools-0.6.1+20161222
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-01-26T07:07:39Z
Finished
--------
I: Built successfully
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| Changes |
+------------------------------------------------------------------------------+
kineticstools_0.6.1+20161222-1_armhf.changes:
---------------------------------------------
Format: 1.8
Date: Sun, 15 Jan 2017 15:53:34 -0800
Source: kineticstools
Binary: kineticstools kineticstools-data python-kineticstools
Architecture: armhf
Version: 0.6.1+20161222-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
kineticstools - detection of DNA modifications
kineticstools-data - detection of DNA modifications -- data files
python-kineticstools - detection of DNA modifications (Python 2 library)
Closes: 848542
Changes:
kineticstools (0.6.1+20161222-1) unstable; urgency=medium
.
[ Andreas Tille ]
* Add fake watch file to silence uscan
.
[ Afif Elghraoui ]
* New upstream revision (Closes: #848542)
* Drop Files-Excluded
* Drop patch applied upstream
* Add README.source to explain how to get new upstream versions
* Update patches without undoing their effects
* autopkgtests: Don't run extra-tests and long-tests
* Suggest python-pybigwig
.
[ Sascha Steinbiss ]
* Fix man page building
* Spelling corrections
* Enable hardening
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python-kineticstools-dbgsym_0.6.1+20161222-1_armhf.deb
------------------------------------------------------
new debian package, version 2.0.
size 5716 bytes: control archive=515 bytes.
491 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: python-kineticstools-dbgsym
Source: kineticstools
Version: 0.6.1+20161222-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 18
Depends: python-kineticstools (= 0.6.1+20161222-1)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/kineticsTools
Description: Debug symbols for python-kineticstools
Auto-Built-Package: debug-symbols
Build-Ids: d29f49f349763401c5247bb8b92a342f90291ebe
drwxr-xr-x root/root 0 2017-01-15 23:53 ./
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 7668 2017-01-15 23:53 ./usr/lib/debug/.build-id/d2/9f49f349763401c5247bb8b92a342f90291ebe.debug
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/share/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-01-15 23:53 ./usr/share/doc/python-kineticstools-dbgsym -> python-kineticstools
python-kineticstools_0.6.1+20161222-1_armhf.deb
-----------------------------------------------
new debian package, version 2.0.
size 48888 bytes: control archive=1963 bytes.
1102 bytes, 21 lines control
2912 bytes, 29 lines md5sums
170 bytes, 9 lines * postinst #!/bin/sh
277 bytes, 14 lines * prerm #!/bin/sh
Package: python-kineticstools
Source: kineticstools
Version: 0.6.1+20161222-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 259
Depends: libc6 (>= 2.4), python (<< 2.8), python (>= 2.7~), python-h5py, python-numpy, python-pbcommand, python-pbcore, python-scipy, python:any (<< 2.8), python:any (>= 2.7.5-5~), kineticstools-data (= 0.6.1+20161222-1)
Suggests: python-pybigwig
Section: python
Priority: optional
Homepage: https://github.com/PacificBiosciences/kineticsTools
Description: detection of DNA modifications (Python 2 library)
Tools for detecting DNA modifications from single molecule, real-time (SMRT®)
sequencing data. This tool implements the P_ModificationDetection module in
SMRT® Portal, used by the RS_Modification_Detection and
RS_Modifications_and_Motif_Detection protocol. Researchers interested in
understanding or extending the modification detection algorithms can use these
tools as a starting point.
.
This package is part of the SMRTAnalysis suite and contains the backend
Python 2 library.
drwxr-xr-x root/root 0 2017-01-15 23:53 ./
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/
-rw-r--r-- root/root 1831 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/PKG-INFO
-rw-r--r-- root/root 1 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/dependency_links.txt
-rw-r--r-- root/root 129 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/entry_points.txt
-rw-r--r-- root/root 1 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/not-zip-safe
-rw-r--r-- root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/requires.txt
-rw-r--r-- root/root 41 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools-0.6.1.egg-info/top_level.txt
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools/
-rw-r--r-- root/root 2638 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/BasicLdaEnricher.py
-rw-r--r-- root/root 35840 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/KineticWorker.py
-rw-r--r-- root/root 3628 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MedakaLdaEnricher.py
-rw-r--r-- root/root 12627 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MixtureEstimationMethods.py
-rw-r--r-- root/root 15729 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ModificationDecode.py
-rw-r--r-- root/root 6939 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteCommon.py
-rw-r--r-- root/root 11759 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/MultiSiteDetection.py
-rw-r--r-- root/root 4918 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/PositiveControlEnricher.py
-rw-r--r-- root/root 6585 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ReferenceUtils.py
-rw-r--r-- root/root 38161 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ResultWriter.py
-rw-r--r-- root/root 9249 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/WorkerProcess.py
-rw-r--r-- root/root 1829 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/__init__.py
-rw-r--r-- root/root 22765 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdModel.py
-rw-r--r-- root/root 32019 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/ipdSummary.py
-rw-r--r-- root/root 2182 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/pipelineTools.py
lrwxrwxrwx root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools/resources -> ../../../../share/kineticstools/resources
-rw-r--r-- root/root 2399 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/sharedArray.py
-rw-r--r-- root/root 7874 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/summarizeModifications.py
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/
-rw-r--r-- root/root 0 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/__init__.py
-rw-r--r-- root/root 6205 2016-12-22 19:12 ./usr/lib/python2.7/dist-packages/kineticsTools/tasks/gather_kinetics_h5.py
-rw-r--r-- root/root 5420 2017-01-15 23:53 ./usr/lib/python2.7/dist-packages/kineticsTools/tree_predict.arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/share/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-01-15 23:53 ./usr/share/doc/python-kineticstools/
-rw-r--r-- root/root 813 2017-01-15 23:53 ./usr/share/doc/python-kineticstools/changelog.Debian.gz
-rw-r--r-- root/root 234 2016-12-22 19:12 ./usr/share/doc/python-kineticstools/changelog.gz
-rw-r--r-- root/root 2036 2017-01-15 22:24 ./usr/share/doc/python-kineticstools/copyright
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 327336
Build-Time: 682
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 589
Job: kineticstools_0.6.1+20161222-1
Machine Architecture: armhf
Package: kineticstools
Package-Time: 1367
Source-Version: 0.6.1+20161222-1
Space: 327336
Status: successful
Version: 0.6.1+20161222-1
--------------------------------------------------------------------------------
Finished at 2017-01-26T07:07:39Z
Build needed 00:22:47, 327336k disc space