Raspbian Package Auto-Building

python-pybedtools → 0.7.8-1 → armhf → 2017-06-24 12:48:57

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| python-pybedtools 0.7.8-1 (armhf)            Sat, 24 Jun 2017 12:35:17 +0000 |
+==============================================================================+

Package: python-pybedtools
Version: 0.7.8-1
Source Version: 0.7.8-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-9979a8dd-16c7-46cf-80f9-df7516405ab1' with '<<CHROOT>>'

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| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [9980 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 21.9 MB in 8s (2709 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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| Fetch source files                                                           |
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Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'python-pybedtools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/python-pybedtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/python-pybedtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 12.5 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main python-pybedtools 0.7.8-1 (dsc) [2322 B]
Get:2 http://172.17.0.1/private buster-staging/main python-pybedtools 0.7.8-1 (tar) [12.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main python-pybedtools 0.7.8-1 (diff) [27.5 kB]
Fetched 12.5 MB in 2s (5020 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pybedtools-6s5UUU/python-pybedtools-0.7.8' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pybedtools-6s5UUU' 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-koLDvU/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-koLDvU/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-koLDvU/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-koLDvU/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (6183 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...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12654 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)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 10), dh-python, bedtools, python3, python3-all, python3-setuptools, python3-dev, python3-pysam, python3-matplotlib, python3-nose, python3-numpy, python3-numpydoc, python3-pandas, python3-yaml, python3-tk, python3-sphinx, cython, r-base-core, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), dh-python, bedtools, python3, python3-all, python3-setuptools, python3-dev, python3-pysam, python3-matplotlib, python3-nose, python3-numpy, python3-numpydoc, python3-pandas, python3-yaml, python3-tk, python3-sphinx, cython, r-base-core, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-python-pybedtools-dummy' in '/<<BUILDDIR>>/resolver-koLDvU/apt_archive/sbuild-build-depends-python-pybedtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-python-pybedtools-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-koLDvU/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Sources [590 B]
Get:5 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ Packages [667 B]
Fetched 2590 B in 0s (7316 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install python-pybedtools build dependencies (apt-based resolver)
-----------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bedtools blt bsdmainutils
  ca-certificates cython debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism docutils-common file fontconfig fontconfig-config
  fonts-lyx gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libblas-common libblas3 libbsd0 libcairo2 libcroco3
  libcurl3 libcurl3-gnutls libdatrie1 libexpat1 libexpat1-dev libffi6
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3
  libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
  libhogweed4 libhts1 libice6 libicu57 libidn2-0 libjbig0 libjpeg62-turbo
  libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14
  libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
  libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib
  libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib
  librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1
  libssl1.0.2 libssl1.1 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5
  libtimedate-perl libtk8.6 libtool libunistring0 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
  libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db mime-support openssl
  po-debconf python python-babel-localedata python-matplotlib-data
  python-minimal python2.7 python2.7-minimal python3 python3-alabaster
  python3-all python3-babel python3-cycler python3-dateutil python3-dev
  python3-docutils python3-imagesize python3-jinja2 python3-markupsafe
  python3-matplotlib python3-minimal python3-nose python3-numpy
  python3-numpydoc python3-pandas python3-pandas-lib python3-pkg-resources
  python3-pygments python3-pyparsing python3-pysam python3-roman
  python3-setuptools python3-six python3-sphinx python3-tk python3-tz
  python3-yaml python3.5 python3.5-dev python3.5-minimal r-base-core sgml-base
  sphinx-common tk8.6-blt2.5 ttf-bitstream-vera ucf unzip x11-common xdg-utils
  xml-core zip zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc filo blt-demo wamerican
  | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev
  libgettextpo-dev groff gnutls-bin krb5-doc krb5-user libjs-jquery-ui-docs
  tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
  www-browser libmail-box-perl python-doc python-tk python2.7-doc
  binfmt-support python3-doc python3-venv python-cycler-doc docutils-doc
  fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
  texlive-latex-base texlive-latex-recommended python-jinja2-doc dvipng ffmpeg
  gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common
  python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo
  python3-gobject python3-pyqt4 python3-scipy python3-sip python3-tornado
  texlive-extra-utils texlive-latex-extra ttf-staypuft python-nose-doc
  gfortran python-numpy-doc python3-numpy-dbg python-pandas-doc
  python-pyparsing-doc python-setuptools-doc python3-sphinx-rtd-theme
  libjs-mathjax texlive-fonts-recommended texlive-generic-extra sphinx-doc tix
  python3-tk-dbg python3.5-venv python3.5-doc ess r-doc-info | r-doc-pdf
  r-mathlib r-base-html sgml-base-doc gvfs-bin
Recommended packages:
  python-dev curl | wget | lynx-cur libglib2.0-data shared-mime-info
  xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules
  libltdl-dev libmail-sendmail-perl python3-pil python3-scipy python3-numexpr
  python3-tables python3-bs4 python3-html5lib python3-lxml r-recommended
  r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bedtools blt bsdmainutils
  ca-certificates cython debhelper dh-autoreconf dh-python
  dh-strip-nondeterminism docutils-common file fontconfig fontconfig-config
  fonts-lyx gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libblas-common libblas3 libbsd0 libcairo2 libcroco3
  libcurl3 libcurl3-gnutls libdatrie1 libexpat1 libexpat1-dev libffi6
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran3
  libglib2.0-0 libgnutls30 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
  libhogweed4 libhts1 libice6 libicu57 libidn2-0 libjbig0 libjpeg62-turbo
  libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14
  libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
  libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-dev libpython3-stdlib
  libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib
  librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh2-1
  libssl1.0.2 libssl1.1 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff5
  libtimedate-perl libtk8.6 libtool libunistring0 libx11-6 libx11-data libxau6
  libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
  libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db mime-support openssl
  po-debconf python python-babel-localedata python-matplotlib-data
  python-minimal python2.7 python2.7-minimal python3 python3-alabaster
  python3-all python3-babel python3-cycler python3-dateutil python3-dev
  python3-docutils python3-imagesize python3-jinja2 python3-markupsafe
  python3-matplotlib python3-minimal python3-nose python3-numpy
  python3-numpydoc python3-pandas python3-pandas-lib python3-pkg-resources
  python3-pygments python3-pyparsing python3-pysam python3-roman
  python3-setuptools python3-six python3-sphinx python3-tk python3-tz
  python3-yaml python3.5 python3.5-dev python3.5-minimal r-base-core
  sbuild-build-depends-python-pybedtools-dummy sgml-base sphinx-common
  tk8.6-blt2.5 ttf-bitstream-vera ucf unzip x11-common xdg-utils xml-core zip
  zlib1g-dev
0 upgraded, 171 newly installed, 0 to remove and 14 not upgraded.
Need to get 128 MB of archives.
After this operation, 349 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-koLDvU/apt_archive ./ sbuild-build-depends-python-pybedtools-dummy 0.invalid.0 [878 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.1-1 [65.2 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.6.3-3.2 [384 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf ttf-bitstream-vera all 1.10-8 [352 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.11.0-6.7 [271 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.11.0-6.7 [313 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.11.0-6.7 [402 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.4-3 [290 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.4-3 [683 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libffi6 armhf 3.2.1-6 [18.7 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.0f-3 [1105 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libpython3.5-minimal armhf 3.5.3-3 [570 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf python3.5-minimal armhf 3.5.3-3 [1447 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.5.3-1 [35.3 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpython3.5-stdlib armhf 3.5.3-3 [2091 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf python3.5 armhf 3.5.3-3 [237 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.5.3-1 [18.6 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-python all 2.20170125 [86.8 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.5.3-1 [21.6 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf sgml-base all 1.29 [14.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2l-2 [893 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
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Get:48 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libnettle6 armhf 3.3-1 [204 kB]
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Get:53 http://172.17.0.1/private buster-staging/main armhf libtasn1-6 armhf 4.12-2 [46.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libgnutls30 armhf 3.5.8-6 [822 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
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Get:58 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
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Get:60 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
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Get:62 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.44+dfsg-5 [85.0 kB]
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Get:66 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf bedtools armhf 2.26.0+dfsg-3 [483 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.6+dfsg-1 [861 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.6-1 [659 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-3 [468 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf blt armhf 2.5.3+dfsg-3 [14.6 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf openssl armhf 1.1.0f-3 [692 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf ca-certificates all 20161130+nmu1 [196 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf cython armhf 0.25.2-1 [1699 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.034-1 [16.4 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.034-1 [10.5 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.11-3 [131 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf xml-core all 0.17 [23.2 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf docutils-common all 0.13.1+dfsg-2 [200 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf fonts-lyx all 2.2.3-1 [197 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libblas-common armhf 3.7.0-2 [14.2 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.3.0-18+rpi1 [166 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.0-2 [107 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.34.0-1 [451 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.12-1 [104 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.12-1 [95.9 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.14.8-1 [688 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libidn2-0 armhf 0.16-1 [59.3 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.23.1-1 [69.1 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-4 [41.4 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.52.1-5 [261 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.10-4 [32.8 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.1-1 [122 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.10-1 [71.7 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.4.2-1 [640 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libhts1 armhf 1.3.2-2+rpi1 [215 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libjs-jquery all 3.1.1-2 [154 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-4 [232 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libjs-underscore all 1.8.3~dfsg-1 [63.8 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libjs-sphinxdoc all 1.4.9-2 [69.5 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.0-2 [1509 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.26-1 [166 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.26-1 [49.3 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.40.5-1 [305 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.40.5-1 [201 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.40.5-1 [190 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libpython3.5 armhf 3.5.3-3 [1173 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libpython3.5-dev armhf 3.5.3-3 [36.9 MB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libpython3-dev armhf 3.5.3-1 [18.7 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.8-2 [218 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.1.7-2 [39.9 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf python-babel-localedata all 2.4.0+dfsg.1-2 [3415 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf python-matplotlib-data all 2.0.0+dfsg1-2 [4414 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf python3-all armhf 3.5.3-1 [934 B]
Get:139 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 33.1.1-1 [137 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf python3-tz all 2016.7-0.3 [27.1 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf python3-babel all 2.4.0+dfsg.1-2 [83.7 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf python3-six all 1.10.0-4 [14.5 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf python3-cycler all 0.10.0-1 [7556 B]
Get:144 http://172.17.0.1/private buster-staging/main armhf python3-dateutil all 2.5.3-2 [45.2 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf python3.5-dev armhf 3.5.3-3 [413 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf python3-dev armhf 3.5.3-1 [1158 B]
Get:147 http://172.17.0.1/private buster-staging/main armhf python3-roman all 2.0.0-2 [8226 B]
Get:148 http://172.17.0.1/private buster-staging/main armhf python3-docutils all 0.13.1+dfsg-2 [371 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf python3-imagesize all 0.7.1-1 [3886 B]
Get:150 http://172.17.0.1/private buster-staging/main armhf python3-markupsafe armhf 0.23-3 [14.5 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf python3-jinja2 all 2.9.5-1 [107 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf python3-pyparsing all 2.1.10+dfsg1-1 [88.6 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf python3-numpy armhf 1:1.12.1-3 [1693 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf python3-matplotlib armhf 2.0.0+dfsg1-2 [1525 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf python3-nose all 1.3.7-2 [132 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf python3-pygments all 2.2.0+dfsg-1 [588 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf python3-alabaster all 0.7.8-1 [18.4 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf sphinx-common all 1.4.9-2 [350 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf python3-sphinx all 1.4.9-2 [433 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf python3-numpydoc all 0.6.0+ds1-1 [30.2 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf python3-pandas-lib armhf 0.19.2-5.1+rpi1 [1944 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf python3-pandas all 0.19.2-5.1+rpi1 [2615 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf python3-pysam armhf 0.9.1.4+ds-1+rpi1 [989 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 33.1.1-1 [215 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf python3-tk armhf 3.5.3-2 [28.1 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf python3-yaml armhf 3.12-1 [93.3 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.3.3-1 [20.9 MB]
Get:171 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
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Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package sbuild-build-depends-python-pybedtools-dummy.
Preparing to unpack .../129-sbuild-build-depends-python-pybedtools-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-python-pybedtools-dummy (0.invalid.0) ...
Setting up libjs-jquery (3.1.1-2) ...
Setting up libnettle6:armhf (3.3-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.23.1-1) ...
Setting up bedtools (2.26.0+dfsg-3) ...
Setting up libjs-underscore (1.8.3~dfsg-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libldap-common (2.4.44+dfsg-5) ...
Setting up libblas-common (3.7.0-2) ...
Setting up libgfortran3:armhf (6.3.0-18+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up unzip (6.0-21) ...
Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up libjs-sphinxdoc (1.4.9-2) ...
Setting up libdatrie1:armhf (0.2.10-4) ...
Setting up libtiff5:armhf (4.0.8-2) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up sgml-base (1.29) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up ucf (3.0036) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up zip (3.0-11) ...
Setting up libfreetype6:armhf (2.6.3-3.2) ...
Setting up libtasn1-6:armhf (4.12-2) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Setting up libhogweed4:armhf (3.3-1) ...
Setting up libgraphite2-3:armhf (1.3.10-1) ...
Setting up libssl1.0.2:armhf (1.0.2l-2) ...
Setting up libyaml-0-2:armhf (0.1.7-2) ...
Setting up libpixman-1-0:armhf (0.34.0-1) ...
Setting up libblas3 (3.7.0-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up python-babel-localedata (2.4.0+dfsg.1-2) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-4) ...
Processing triggers for systemd (232-25) ...
Setting up openssl (1.1.0f-3) ...
Setting up sphinx-common (1.4.9-2) ...
Setting up libexpat1-dev:armhf (2.2.1-1) ...
Setting up ttf-bitstream-vera (1.10-8) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up libtcl8.6:armhf (8.6.6+dfsg-1) ...
Setting up libthai-data (0.1.26-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up xml-core (0.17) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 x11-common (1:7.7+19) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up xdg-utils (1.1.1-1) ...
Setting up ca-certificates (20161130+nmu1) ...
Updating certificates in /etc/ssl/certs...
166 added, 0 removed; done.
Setting up libx11-data (2:1.6.4-3) ...
Setting up libpython2.7-stdlib:armhf (2.7.13-2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up fonts-lyx (2.2.3-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up libpaper1:armhf (1.1.24+nmu5) ...

Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24+nmu5) ...
Setting up fontconfig-config (2.11.0-6.7) ...
Setting up libidn2-0:armhf (0.16-1) ...
Setting up python-matplotlib-data (2.0.0+dfsg1-2) ...
Setting up libpsl5:armhf (0.17.0-4) ...
Setting up liblapack3 (3.7.0-2) ...
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 (2.50.3-2) ...
No schema files found: doing nothing.
Setting up libpython3.5-stdlib:armhf (3.5.3-3) ...
Setting up python2.7 (2.7.13-2) ...
Setting up libharfbuzz0b:armhf (1.4.2-1) ...
Setting up autoconf (2.69-10) ...
Setting up libthai0:armhf (0.1.26-1) ...
Setting up file (1:5.30-1) ...
Setting up libkrb5support0:armhf (1.15-1) ...
Setting up libcroco3:armhf (0.6.11-3) ...
Setting up libpython-stdlib:armhf (2.7.13-2) ...
Setting up libp11-kit0:armhf (0.23.3-5) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxcb1:armhf (1.12-1) ...
Setting up python (2.7.13-2) ...
Setting up libtool (2.4.6-2) ...
Setting up python3.5 (3.5.3-3) ...
Setting up libpython3-stdlib:armhf (3.5.3-1) ...
Setting up libfontconfig1:armhf (2.11.0-6.7) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libk5crypto3:armhf (1.15-1) ...
Setting up libxcb-render0:armhf (1.12-1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libpython3.5:armhf (3.5.3-3) ...
Setting up libgnutls30:armhf (3.5.8-6) ...
Setting up libx11-6:armhf (2:1.6.4-3) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up libpython3.5-dev:armhf (3.5.3-3) ...
Setting up cython (0.25.2-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-5) ...
Setting up libxcb-shm0:armhf (1.12-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libkrb5-3:armhf (1.15-1) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up python3.5-dev (3.5.3-3) ...
Setting up fontconfig (2.11.0-6.7) ...
Regenerating fonts cache... done.
Setting up libpython3-dev:armhf (3.5.3-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.15-1) ...
Setting up libpango-1.0-0:armhf (1.40.5-1) ...
Setting up libcairo2:armhf (1.14.8-1) ...
Setting up libcurl3:armhf (7.52.1-5) ...
Setting up libcurl3-gnutls:armhf (7.52.1-5) ...
Setting up libtk8.6:armhf (8.6.6-1) ...
Setting up libpangoft2-1.0-0:armhf (1.40.5-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-3) ...
Setting up blt (2.5.3+dfsg-3) ...
Setting up libhts1:armhf (1.3.2-2+rpi1) ...
Setting up libpangocairo-1.0-0:armhf (1.40.5-1) ...
Setting up r-base-core (3.3.3-1) ...

Creating config file /etc/R/Renviron with new version
Processing triggers for sgml-base (1.29) ...
Setting up docutils-common (0.13.1+dfsg-2) ...
Processing triggers for sgml-base (1.29) ...
Setting up dh-autoreconf (14) ...
Setting up python3 (3.5.3-1) ...
Setting up python3-numpy (1:1.12.1-3) ...
Setting up python3-alabaster (0.7.8-1) ...
Setting up python3-six (1.10.0-4) ...
Setting up python3-pyparsing (2.1.10+dfsg1-1) ...
Setting up python3-cycler (0.10.0-1) ...
Setting up python3-dev (3.5.3-1) ...
Setting up python3-pkg-resources (33.1.1-1) ...
Setting up python3-markupsafe (0.23-3) ...
Setting up python3-pandas-lib (0.19.2-5.1+rpi1) ...
Setting up dh-strip-nondeterminism (0.034-1) ...
Setting up python3-pysam (0.9.1.4+ds-1+rpi1) ...
Setting up python3-nose (1.3.7-2) ...
Setting up python3-all (3.5.3-1) ...
Setting up python3-jinja2 (2.9.5-1) ...
Setting up python3-tk:armhf (3.5.3-2) ...
Setting up python3-setuptools (33.1.1-1) ...
Setting up dh-python (2.20170125) ...
Setting up python3-tz (2016.7-0.3) ...
Setting up python3-dateutil (2.5.3-2) ...
Setting up python3-pygments (2.2.0+dfsg-1) ...
Setting up python3-yaml (3.12-1) ...
Setting up debhelper (10.2.5) ...
Setting up python3-roman (2.0.0-2) ...
Setting up python3-imagesize (0.7.1-1) ...
Setting up python3-babel (2.4.0+dfsg.1-2) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-docutils (0.13.1+dfsg-2) ...
update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode
update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode
Setting up python3-pandas (0.19.2-5.1+rpi1) ...
Setting up python3-matplotlib (2.0.0+dfsg1-2) ...
Setting up python3-sphinx (1.4.9-2) ...
Setting up python3-numpydoc (0.6.0+ds1-1) ...
Setting up sbuild-build-depends-python-pybedtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Processing triggers for systemd (232-25) ...
Processing triggers for ca-certificates (20161130+nmu1) ...
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 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-5 dpkg-dev_1.18.24 g++-6_6.3.0-18+rpi1 gcc-6_6.3.0-18+rpi1 libc6-dev_2.24-11+deb9u1 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 bedtools_2.26.0+dfsg-3 binutils_2.28-5 blt_2.5.3+dfsg-3 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-18+rpi1 cython_0.25.2-1 dash_0.5.8-2.4 debconf_1.5.61 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.034-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 docutils-common_0.13.1+dfsg-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20161106-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-lyx_2.2.3-1 g++_4:6.3.0-4 g++-6_6.3.0-18+rpi1 gcc_4:6.3.0-4 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.3.0-18+rpi1 gcc-6-base_6.3.0-18+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan3_6.3.0-18+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-18+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-2 libaudit1_1:2.6.7-2 libblas-common_3.7.0-2 libblas3_3.7.0-2 libblkid1_2.29.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-11+deb9u1 libc-dev-bin_2.24-11+deb9u1 libc6_2.24-11+deb9u1 libc6-dev_2.24-11+deb9u1 libcairo2_1.14.8-1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.3.0-18+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.3-4 libcurl3_7.52.1-5 libcurl3-gnutls_7.52.1-5 libdatrie1_0.2.10-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.74-1 libexpat1_2.2.1-1 libexpat1-dev_2.2.1-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.034-1 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3.2 libgcc-6-dev_6.3.0-18+rpi1 libgcc1_1:6.3.0-18+rpi1 libgcrypt20_1.7.6-2 libgdbm3_1.8.3-14 libgfortran3_6.3.0-18+rpi1 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-6 libgomp1_6.3.0-18+rpi1 libgpg-error0_1.26-2 libgraphite2-3_1.3.10-1 libgssapi-krb5-2_1.15-1 libharfbuzz0b_1.4.2-1 libhogweed4_3.3-1 libhts1_1.3.2-2+rpi1 libice6_2:1.0.9-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.5.1-2 libjs-jquery_3.1.1-2 libjs-jquery-ui_1.12.1+dfsg-4 libjs-sphinxdoc_1.4.9-2 libjs-underscore_1.8.3~dfsg-1 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 liblapack3_3.7.0-2 libldap-2.4-2_2.4.44+dfsg-5 libldap-common_2.4.44+dfsg-5 liblocale-gettext-perl_1.07-3+b1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1 libnghttp2-14_1.23.1-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.3-1 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpango-1.0-0_1.40.5-1 libpangocairo-1.0-0_1.40.5-1 libpangoft2-1.0-0_1.40.5-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre3_2:8.39-3 libperl5.24_5.24.1-3 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libplymouth4_0.9.2-4 libpng16-16_1.6.28-1 libprocps6_2:3.3.12-3 libpsl5_0.17.0-4 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-dev_3.5.3-1 libpython3-stdlib_3.5.3-1 libpython3.5_3.5.3-3 libpython3.5-dev_3.5.3-3 libpython3.5-minimal_3.5.3-3 libpython3.5-stdlib_3.5.3-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 libsystemd0_232-25 libtasn1-6_4.12-2 libtcl8.6_8.6.6+dfsg-1 libtext-charwidth-perl_0.04-7+b7 libtext-iconv-perl_1.7-5+b8 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.26-1 libthai0_0.1.26-1 libtiff5_4.0.8-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtk8.6_8.6.6-1 libtool_2.4.6-2 libubsan0_6.3.0-18+rpi1 libudev1_232-25 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-2.2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libyaml-0-2_0.1.7-2 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-1 mountall_2.54 multiarch-support_2.24-11+deb9u1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-3 perl-base_5.24.1-3 perl-modules-5.24_5.24.1-3 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-babel-localedata_2.4.0+dfsg.1-2 python-matplotlib-data_2.0.0+dfsg1-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1 python3-alabaster_0.7.8-1 python3-all_3.5.3-1 python3-babel_2.4.0+dfsg.1-2 python3-cycler_0.10.0-1 python3-dateutil_2.5.3-2 python3-dev_3.5.3-1 python3-docutils_0.13.1+dfsg-2 python3-imagesize_0.7.1-1 python3-jinja2_2.9.5-1 python3-markupsafe_0.23-3 python3-matplotlib_2.0.0+dfsg1-2 python3-minimal_3.5.3-1 python3-nose_1.3.7-2 python3-numpy_1:1.12.1-3 python3-numpydoc_0.6.0+ds1-1 python3-pandas_0.19.2-5.1+rpi1 python3-pandas-lib_0.19.2-5.1+rpi1 python3-pkg-resources_33.1.1-1 python3-pygments_2.2.0+dfsg-1 python3-pyparsing_2.1.10+dfsg1-1 python3-pysam_0.9.1.4+ds-1+rpi1 python3-roman_2.0.0-2 python3-setuptools_33.1.1-1 python3-six_1.10.0-4 python3-sphinx_1.4.9-2 python3-tk_3.5.3-2 python3-tz_2016.7-0.3 python3-yaml_3.12-1 python3.5_3.5.3-3 python3.5-dev_3.5.3-3 python3.5-minimal_3.5.3-3 r-base-core_3.3.3-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pybedtools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sgml-base_1.29 sphinx-common_1.4.9-2 systemd_232-25 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tk8.6-blt2.5_2.5.3+dfsg-3 ttf-bitstream-vera_1.10-8 tzdata_2017b-1 ucf_3.0036 udev_232-25 unzip_6.0-21 util-linux_2.29.2-1 x11-common_1:7.7+19 xdg-utils_1.1.1-1 xml-core_0.17 xz-utils_5.2.2-1.2 zip_3.0-11 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

+------------------------------------------------------------------------------+
| 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 15:24:21 2017 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pybedtools_0.7.8-1.dsc
dpkg-source: info: extracting python-pybedtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-pybedtools_0.7.8.orig.tar.gz
dpkg-source: info: unpacking python-pybedtools_0.7.8-1.debian.tar.xz
dpkg-source: info: applying spelling
dpkg-source: info: applying enable-package-data
dpkg-source: info: applying disable-write-version
dpkg-source: info: applying disable-test-156
dpkg-source: info: applying rename-scripts

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-9979a8dd-16c7-46cf-80f9-df7516405ab1
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package python-pybedtools
dpkg-buildpackage: info: source version 0.7.8-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build python-pybedtools-0.7.8
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
   dh_testdir -O--buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:184: python3.5 setup.py clean 
running clean
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python3,sphinxdoc --buildsystem=pybuild
   dh_testdir -a -O--buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python3.5 setup.py config 
warning: cbedtools.pyx:766:16: Unreachable code
Processing pybedtools/_Window.pyx
Processing pybedtools/featurefuncs.pyx
Processing pybedtools/cbedtools.pyx
Cythonizing sources
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:184: /usr/bin/python3 setup.py build 
pybedtools/_Window.pyx has not changed
pybedtools/featurefuncs.pyx has not changed
pybedtools/cbedtools.pyx has not changed
Cythonizing sources
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/logger.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/helpers.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/stats.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/settings.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_scripts.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test1.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
creating /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/classifier.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/contrib
creating /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/intron_exon_reads.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/py_ms_example.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/venn_mpl.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/annotate.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/peak_pie.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
copying pybedtools/scripts/venn_gchart.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/scripts
creating /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
running egg_info
creating pybedtools.egg-info
writing pybedtools.egg-info/PKG-INFO
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
writing entry points to pybedtools.egg-info/entry_points.txt
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
copying pybedtools/_Window.c -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/cbedtools.cxx -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/featurefuncs.cxx -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/data
copying pybedtools/_Window.pyx -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools
copying pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
copying pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build
creating build/temp.linux-armhf-3.5
creating build/temp.linux-armhf-3.5/src
creating build/temp.linux-armhf-3.5/pybedtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/bedFile.cpp -o build/temp.linux-armhf-3.5/src/bedFile.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/fileType.cpp -o build/temp.linux-armhf-3.5/src/fileType.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/gzstream.cpp -o build/temp.linux-armhf-3.5/src/gzstream.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c pybedtools/cbedtools.cxx -o build/temp.linux-armhf-3.5/pybedtools/cbedtools.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
pybedtools/cbedtools.cxx:8701:12: warning: 'int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject*)' defined but not used [-Wunused-function]
 static int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject *__pyx_v_self) {
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/src/bedFile.o build/temp.linux-armhf-3.5/src/fileType.o build/temp.linux-armhf-3.5/src/gzstream.o build/temp.linux-armhf-3.5/pybedtools/cbedtools.o -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/cbedtools.cpython-35m-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/bedFile.cpp -o build/temp.linux-armhf-3.5/src/bedFile.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/fileType.cpp -o build/temp.linux-armhf-3.5/src/fileType.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/gzstream.cpp -o build/temp.linux-armhf-3.5/src/gzstream.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c pybedtools/featurefuncs.cxx -o build/temp.linux-armhf-3.5/pybedtools/featurefuncs.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/src/bedFile.o build/temp.linux-armhf-3.5/src/fileType.o build/temp.linux-armhf-3.5/src/gzstream.o build/temp.linux-armhf-3.5/pybedtools/featurefuncs.o -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/featurefuncs.cpython-35m-arm-linux-gnueabihf.so
python3 setup.py develop --user
pybedtools/_Window.pyx has not changed
pybedtools/featurefuncs.pyx has not changed
pybedtools/cbedtools.pyx has not changed
Cythonizing sources
running develop
running egg_info
writing requirements to pybedtools.egg-info/requires.txt
writing pybedtools.egg-info/PKG-INFO
writing entry points to pybedtools.egg-info/entry_points.txt
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing top-level names to pybedtools.egg-info/top_level.txt
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
running build_ext
building 'pybedtools.featurefuncs' extension
creating build/temp.linux-armv8l-3.5
creating build/temp.linux-armv8l-3.5/src
creating build/temp.linux-armv8l-3.5/pybedtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/bedFile.cpp -o build/temp.linux-armv8l-3.5/src/bedFile.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/fileType.cpp -o build/temp.linux-armv8l-3.5/src/fileType.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/gzstream.cpp -o build/temp.linux-armv8l-3.5/src/gzstream.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c pybedtools/featurefuncs.cxx -o build/temp.linux-armv8l-3.5/pybedtools/featurefuncs.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv8l-3.5/src/bedFile.o build/temp.linux-armv8l-3.5/src/fileType.o build/temp.linux-armv8l-3.5/src/gzstream.o build/temp.linux-armv8l-3.5/pybedtools/featurefuncs.o -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/featurefuncs.cpython-35m-arm-linux-gnueabihf.so
building 'pybedtools.cbedtools' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/bedFile.cpp -o build/temp.linux-armv8l-3.5/src/bedFile.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/fileType.cpp -o build/temp.linux-armv8l-3.5/src/fileType.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c src/gzstream.cpp -o build/temp.linux-armv8l-3.5/src/gzstream.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/ -I/usr/include/python3.5m -c pybedtools/cbedtools.cxx -o build/temp.linux-armv8l-3.5/pybedtools/cbedtools.o
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
pybedtools/cbedtools.cxx:8701:12: warning: 'int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject*)' defined but not used [-Wunused-function]
 static int __pyx_pw_10pybedtools_9cbedtools_8Interval_25__nonzero__(PyObject *__pyx_v_self) {
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv8l-3.5/src/bedFile.o build/temp.linux-armv8l-3.5/src/fileType.o build/temp.linux-armv8l-3.5/src/gzstream.o build/temp.linux-armv8l-3.5/pybedtools/cbedtools.o -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/cbedtools.cpython-35m-arm-linux-gnueabihf.so
Creating /<<PKGBUILDDIR>>/fakehome/.local/lib/python3.5/site-packages/pybedtools.egg-link (link to .)
Adding pybedtools 0.7.8 to easy-install.pth file
Installing pybedtools-intersection_matrix script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing pybedtools-venn_mpl script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing pybedtools-venn_gchart script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing pybedtools-intron_exon_reads script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing pybedtools-annotate script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing pybedtools-peak_pie script to /<<PKGBUILDDIR>>/fakehome/.local/bin

Installed /<<PKGBUILDDIR>>
Processing dependencies for pybedtools==0.7.8
Searching for six==1.10.0
Best match: six 1.10.0
Adding six 1.10.0 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.7.8
python3 setup.py build_sphinx
pybedtools/_Window.pyx has not changed
pybedtools/featurefuncs.pyx has not changed
pybedtools/cbedtools.pyx has not changed
Cythonizing sources
running build_sphinx
creating /<<PKGBUILDDIR>>/build/sphinx
creating /<<PKGBUILDDIR>>/build/sphinx/doctrees
creating /<<PKGBUILDDIR>>/build/sphinx/html
Running Sphinx v1.4.9
loading pickled environment... not yet created
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.contrib.plotting.Track.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
[autosummary] generating autosummary for: /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.annotate.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.intersection_matrix.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.intron_exon_reads.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.py_ms_example.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.venn_gchart.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.scripts.venn_mpl.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 49 source files that are out of date
updating environment: 166 added, 0 changed, 0 removed
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build succeeded, 12 warnings.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild pybuild:219: cp /<<PKGBUILDDIR>>/debian/mpl-expected.png /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/
I: pybuild base:184: cd /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose --attr '!url'
...................................F................................F.....F......F........S.........................................................................................................................................................................................................................................................................................................................................................................................FFFF.............S..
======================================================================
FAIL: pybedtools.test.test1.test_randomstats
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test1.py", line 793, in test_randomstats
    assert results['percentile'] == 89.5
AssertionError

======================================================================
FAIL: pybedtools.test.test1.test_random
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test1.py", line 1393, in test_random
    """)
AssertionError

======================================================================
FAIL: pybedtools.test.test1.test_reldist
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test1.py", line 1458, in test_reldist
    assert results == {'reldist': [0.15, 0.21, 0.28], 'count': [1, 1, 1], 'total': [3, 3, 3], 'fraction': [0.333, 0.333, 0.333]}, results
AssertionError: {'reldist': [0.16, 0.21], 'total': [3, 3], 'count': [1, 2], 'fraction': [0.333, 0.667]}

======================================================================
FAIL: pybedtools.test.test1.test_fisher
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test1.py", line 1760, in test_fisher
    """, c
AssertionError: # Number of query intervals: 4
# Number of db intervals: 2
# Number of overlaps: 3
# Number of possible intervals (estimated): 3543090
# phyper(3 - 1, 4, 3543090 - 4, 2, lower.tail=F)
# Contingency Table Of Counts
#_________________________________________
#           |  in -b       | not in -b    |
#     in -a | 3            | 1            |
# not in -a | 0            | 3543086      |
#_________________________________________
# p-values for fisher's exact test
left	right	two-tail	ratio
1	5.3959e-19	5.3959e-19	inf


======================================================================
FAIL: sample, i=filename ibam=False, {'n': 2, 'seed': 1}
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test_iter.py", line 68, in run
    assert res == expected
AssertionError: 
-------------------- >> begin captured stdout << ---------------------
/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/tmp/pybedtools.5yrz3n4p.tmp
Method call:
BedTool.sample(n=2, seed=1)
Got:
chr2L	70	75	None	255	+
chr2L	70	75	None	255	-

Expected:
chr2L	140	145	None	255	-
chr2L	70	75	None	255	-

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L	70	75	None	255	+
 +chr2L	140	145	None	255	-
  chr2L	70	75	None	255	-
 Showing special characters:
Got:
chr2L\t70\t75\tNone\t255\t+\n
chr2L\t70\t75\tNone\t255\t-\n

Expected:
chr2L\t140\t145\tNone\t255\t-\n
chr2L\t70\t75\tNone\t255\t-\n

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L\t70\t75\tNone\t255\t+\n
 +chr2L\t140\t145\tNone\t255\t-\n
  chr2L\t70\t75\tNone\t255\t-\n
 
--------------------- >> end captured stdout << ----------------------

======================================================================
FAIL: sample, i=generator ibam=False, {'n': 2, 'seed': 1}
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test_iter.py", line 68, in run
    assert res == expected
AssertionError: 
-------------------- >> begin captured stdout << ---------------------
/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/tmp/pybedtools.mkh3sw9x.tmp
Method call:
BedTool.sample(n=2, seed=1)
Got:
chr2L	70	75	None	255	+
chr2L	70	75	None	255	-

Expected:
chr2L	140	145	None	255	-
chr2L	70	75	None	255	-

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L	70	75	None	255	+
 +chr2L	140	145	None	255	-
  chr2L	70	75	None	255	-
 Showing special characters:
Got:
chr2L\t70\t75\tNone\t255\t+\n
chr2L\t70\t75\tNone\t255\t-\n

Expected:
chr2L\t140\t145\tNone\t255\t-\n
chr2L\t70\t75\tNone\t255\t-\n

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L\t70\t75\tNone\t255\t+\n
 +chr2L\t140\t145\tNone\t255\t-\n
  chr2L\t70\t75\tNone\t255\t-\n
 
--------------------- >> end captured stdout << ----------------------

======================================================================
FAIL: sample, i=stream ibam=False, {'n': 2, 'seed': 1}
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test_iter.py", line 68, in run
    assert res == expected
AssertionError: 
-------------------- >> begin captured stdout << ---------------------
/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/tmp/pybedtools.tmkjadot.tmp
Method call:
BedTool.sample(n=2, seed=1)
Got:
chr2L	70	75	None	255	+
chr2L	70	75	None	255	-

Expected:
chr2L	140	145	None	255	-
chr2L	70	75	None	255	-

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L	70	75	None	255	+
 +chr2L	140	145	None	255	-
  chr2L	70	75	None	255	-
 Showing special characters:
Got:
chr2L\t70\t75\tNone\t255\t+\n
chr2L\t70\t75\tNone\t255\t-\n

Expected:
chr2L\t140\t145\tNone\t255\t-\n
chr2L\t70\t75\tNone\t255\t-\n

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L\t70\t75\tNone\t255\t+\n
 +chr2L\t140\t145\tNone\t255\t-\n
  chr2L\t70\t75\tNone\t255\t-\n
 
--------------------- >> end captured stdout << ----------------------

======================================================================
FAIL: sample, i=gzip ibam=False, {'n': 2, 'seed': 1}
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/test_iter.py", line 68, in run
    assert res == expected
AssertionError: 
-------------------- >> begin captured stdout << ---------------------
/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/pybedtools/test/tmp/pybedtools.en71vgvo.tmp
Method call:
BedTool.sample(n=2, seed=1)
Got:
chr2L	70	75	None	255	+
chr2L	70	75	None	255	-

Expected:
chr2L	140	145	None	255	-
chr2L	70	75	None	255	-

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L	70	75	None	255	+
 +chr2L	140	145	None	255	-
  chr2L	70	75	None	255	-
 Showing special characters:
Got:
chr2L\t70\t75\tNone\t255\t+\n
chr2L\t70\t75\tNone\t255\t-\n

Expected:
chr2L\t140\t145\tNone\t255\t-\n
chr2L\t70\t75\tNone\t255\t-\n

Diff:
--- 
 +++ 
 @@ -1,2 +1,2 @@
 -chr2L\t70\t75\tNone\t255\t+\n
 +chr2L\t140\t145\tNone\t255\t-\n
  chr2L\t70\t75\tNone\t255\t-\n
 
--------------------- >> end captured stdout << ----------------------

----------------------------------------------------------------------
Ran 488 tests in 54.988s

FAILED (SKIP=2, failures=8)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose --attr '!url'
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned exit code 13
debian/rules:16: recipe for target 'build-arch' failed
make: *** [build-arch] Error 25
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-06-24T12:48:56Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 57188
Build-Time: 260
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 540
Job: python-pybedtools_0.7.8-1
Machine Architecture: armhf
Package: python-pybedtools
Package-Time: 819
Source-Version: 0.7.8-1
Space: 57188
Status: attempted
Version: 0.7.8-1
--------------------------------------------------------------------------------
Finished at 2017-06-24T12:48:56Z
Build needed 00:13:39, 57188k disk space

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