Raspbian Package Auto-Building

Build log for python-pysam (0.9.0+ds-1) on armhf

python-pysam → 0.9.0+ds-1 → armhf → 2016-04-10 03:46:57 

sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-02

+==============================================================================+
| python-pysam 0.9.0+ds-1 (armhf)                            10 Apr 2016 02:25 |
+==============================================================================+

Package: python-pysam
Version: 0.9.0+ds-1
Source Version: 0.9.0+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/python-pysam-duKVU9/python-pysam-0.9.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-duKVU9' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-215c4778-93f5-4a43-b8cc-e1b783f6fdf3' 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 [8889 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 19.9 MB in 21s (934 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: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/python-pysam.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2279 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main python-pysam 0.9.0+ds-1 (dsc) [2434 B]
Get:2 http://172.17.0.1/private stretch-staging/main python-pysam 0.9.0+ds-1 (tar) [2268 kB]
Get:3 http://172.17.0.1/private stretch-staging/main python-pysam 0.9.0+ds-1 (diff) [9284 B]
Fetched 2279 kB in 0s (7451 kB/s)
Download complete and in download only mode

Check architectures
-------------------


Check dependencies
------------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-1N5DSY/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ Packages [505 B]
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 NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 49 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-1N5DSY/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13554 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3), bcftools (>= 1.3), python-nose, python3-nose
Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3), bcftools (>= 1.3), python-nose, python3-nose
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-rnsE0y/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Sources [275 B]
Get:5 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ Packages [593 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

+------------------------------------------------------------------------------+
| Install python-pysam 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 bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
  libcroco3 libexpat1 libexpat1-dev libffi6 libfile-stripnondeterminism-perl
  libglib2.0-0 libgsl2 libhts-dev libhts1 libicu55 libmagic1 libmpdec2
  libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7
  libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
  libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev
  libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libsqlite3-0
  libssl1.0.2 libtool libunistring0 libxml2 m4 man-db mime-support po-debconf
  python python-all python-all-dev python-dev python-minimal python-nose
  python-pkg-resources python-setuptools python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-dev
  python3-minimal python3-nose python3-pkg-resources python3-setuptools
  python3.5 python3.5-dev python3.5-minimal samtools tabix zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib
  texlive-latex-recommended wamerican | wordlist whois vacation cython-doc
  dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc
  | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gfortran
  | fortran95-compiler gcj-jdk less www-browser libmail-box-perl python-doc
  python-tk python-coverage python-nose-doc python-setuptools-doc
  python2.7-doc binfmt-support python3-doc python3-tk python3-venv
  python3.5-venv python3.5-doc
Recommended packages:
  curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
  libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
  libcroco3 libexpat1 libexpat1-dev libffi6 libfile-stripnondeterminism-perl
  libglib2.0-0 libgsl2 libhts-dev libhts1 libicu55 libmagic1 libmpdec2
  libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7
  libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
  libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev
  libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libsqlite3-0
  libssl1.0.2 libtool libunistring0 libxml2 m4 man-db mime-support po-debconf
  python python-all python-all-dev python-dev python-minimal python-nose
  python-pkg-resources python-setuptools python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-dev
  python3-minimal python3-nose python3-pkg-resources python3-setuptools
  python3.5 python3.5-dev python3.5-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 82 newly installed, 0 to remove and 49 not upgraded.
Need to get 100 MB/100 MB of archives.
After this operation, 220 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-rnsE0y/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [854 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-7 [381 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-7 [1160 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.59 [36.4 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.1-1 [60.4 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.11.1-1 [457 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-1 [886 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-7 [1818 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-7 [268 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.1-5 [553 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.1-5 [1333 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.1-3 [35.2 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.1-5 [2063 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.1-5 [194 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.1-3 [18.6 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20151103 [76.9 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.1-3 [21.6 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libpython2.7 armhf 2.7.11-7 [908 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libgsl2 armhf 2.1+dfsg-2 [697 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3-2+rpi1 [207 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf bcftools armhf 1.3-3 [273 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf cython armhf 0.23.4+git4-g7eed8d8-1 [1446 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf cython3 armhf 0.23.4+git4-g7eed8d8-1 [1453 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.1.1-1 [117 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3-2+rpi1 [260 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-dev armhf 2.7.11-7 [27.1 MB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libpython-dev armhf 2.7.11-1 [19.6 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libpython-all-dev armhf 2.7.11-1 [958 B]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libpython3.5 armhf 3.5.1-5 [1160 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-dev armhf 3.5.1-5 [36.4 MB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libpython3-dev armhf 3.5.1-3 [18.7 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libpython3-all-dev armhf 3.5.1-3 [964 B]
Get:66 http://172.17.0.1/private stretch-staging/main armhf python-all armhf 2.7.11-1 [940 B]
Get:67 http://172.17.0.1/private stretch-staging/main armhf python2.7-dev armhf 2.7.11-7 [279 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf python-dev armhf 2.7.11-1 [1138 B]
Get:69 http://172.17.0.1/private stretch-staging/main armhf python-all-dev armhf 2.7.11-1 [962 B]
Get:70 http://172.17.0.1/private stretch-staging/main armhf python-pkg-resources all 18.8-1 [100 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf python-nose all 1.3.7-1 [132 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf python-setuptools all 18.8-1 [202 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf python3-all armhf 3.5.1-3 [940 B]
Get:74 http://172.17.0.1/private stretch-staging/main armhf python3.5-dev armhf 3.5.1-5 [418 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf python3-dev armhf 3.5.1-3 [1154 B]
Get:76 http://172.17.0.1/private stretch-staging/main armhf python3-all-dev armhf 3.5.1-3 [962 B]
Get:77 http://172.17.0.1/private stretch-staging/main armhf python3-pkg-resources all 18.8-1 [71.1 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf python3-nose all 1.3.7-1 [132 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf python3-setuptools all 18.8-1 [120 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3-1 [215 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf tabix armhf 1.3-2+rpi1 [192 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 100 MB in 9s (10.1 MB/s)
Selecting previously unselected package groff-base.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13554 files and directories currently installed.)
Preparing to unpack .../groff-base_1.22.3-7_armhf.deb ...
Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../libbsd0_0.8.2-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.2-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.10_armhf.deb ...
Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armhf.deb ...
Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../libpython2.7-minimal_2.7.11-7_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.11-7) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../python2.7-minimal_2.7.11-7_armhf.deb ...
Unpacking python2.7-minimal (2.7.11-7) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../python-minimal_2.7.11-1_armhf.deb ...
Unpacking python-minimal (2.7.11-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../mime-support_3.59_all.deb ...
Unpacking mime-support (3.59) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.1.1-1_armhf.deb ...
Unpacking libexpat1:armhf (2.1.1-1) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.2.1-4_armhf.deb ...
Unpacking libffi6:armhf (3.2.1-4) ...
Selecting previously unselected package libsqlite3-0:armhf.
Preparing to unpack .../libsqlite3-0_3.11.1-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.11.1-1) ...
Selecting previously unselected package libssl1.0.2:armhf.
Preparing to unpack .../libssl1.0.2_1.0.2g-1_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2g-1) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../libpython2.7-stdlib_2.7.11-7_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.11-7) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.11-7_armhf.deb ...
Unpacking python2.7 (2.7.11-7) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../libpython-stdlib_2.7.11-1_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.11-1) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up libpython2.7-minimal:armhf (2.7.11-7) ...
Setting up python2.7-minimal (2.7.11-7) ...
Setting up python-minimal (2.7.11-1) ...
Selecting previously unselected package python.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14923 files and directories currently installed.)
Preparing to unpack .../python_2.7.11-1_armhf.deb ...
Unpacking python (2.7.11-1) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5.2_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5.2) ...
Selecting previously unselected package libpython3.5-minimal:armhf.
Preparing to unpack .../libpython3.5-minimal_3.5.1-5_armhf.deb ...
Unpacking libpython3.5-minimal:armhf (3.5.1-5) ...
Selecting previously unselected package python3.5-minimal.
Preparing to unpack .../python3.5-minimal_3.5.1-5_armhf.deb ...
Unpacking python3.5-minimal (3.5.1-5) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../python3-minimal_3.5.1-3_armhf.deb ...
Unpacking python3-minimal (3.5.1-3) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../libmpdec2_2.4.2-1_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.2-1) ...
Selecting previously unselected package libpython3.5-stdlib:armhf.
Preparing to unpack .../libpython3.5-stdlib_3.5.1-5_armhf.deb ...
Unpacking libpython3.5-stdlib:armhf (3.5.1-5) ...
Selecting previously unselected package python3.5.
Preparing to unpack .../python3.5_3.5.1-5_armhf.deb ...
Unpacking python3.5 (3.5.1-5) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../libpython3-stdlib_3.5.1-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.5.1-3) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../dh-python_2.20151103_all.deb ...
Unpacking dh-python (2.20151103) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up libssl1.0.2:armhf (1.0.2g-1) ...
Setting up libpython3.5-minimal:armhf (3.5.1-5) ...
Setting up libexpat1:armhf (2.1.1-1) ...
Setting up python3.5-minimal (3.5.1-5) ...
Setting up python3-minimal (3.5.1-3) ...
Processing triggers for libc-bin (2.22-3) ...
Selecting previously unselected package python3.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 15909 files and directories currently installed.)
Preparing to unpack .../python3_3.5.1-3_armhf.deb ...
Unpacking python3 (3.5.1-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.25-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_armhf.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armhf.deb ...
Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libpython2.7:armhf.
Preparing to unpack .../libpython2.7_2.7.11-7_armhf.deb ...
Unpacking libpython2.7:armhf (2.7.11-7) ...
Selecting previously unselected package libicu55:armhf.
Preparing to unpack .../libicu55_55.1-7_armhf.deb ...
Unpacking libicu55:armhf (55.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armhf.deb ...
Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../libsigsegv2_2.10-5_armhf.deb ...
Unpacking libsigsegv2:armhf (2.10-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../archives/m4_1.4.17-5_armhf.deb ...
Unpacking m4 (1.4.17-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../autoconf_2.69-10_all.deb ...
Unpacking autoconf (2.69-10) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
Unpacking autotools-dev (20150820.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
Unpacking automake (1:1.15-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libgsl2:armhf.
Preparing to unpack .../libgsl2_2.1+dfsg-2_armhf.deb ...
Unpacking libgsl2:armhf (2.1+dfsg-2) ...
Selecting previously unselected package libhts1:armhf.
Preparing to unpack .../libhts1_1.3-2+rpi1_armhf.deb ...
Unpacking libhts1:armhf (1.3-2+rpi1) ...
Selecting previously unselected package bcftools.
Preparing to unpack .../bcftools_1.3-3_armhf.deb ...
Unpacking bcftools (1.3-3) ...
Selecting previously unselected package cython.
Preparing to unpack .../cython_0.23.4+git4-g7eed8d8-1_armhf.deb ...
Unpacking cython (0.23.4+git4-g7eed8d8-1) ...
Selecting previously unselected package cython3.
Preparing to unpack .../cython3_0.23.4+git4-g7eed8d8-1_armhf.deb ...
Unpacking cython3 (0.23.4+git4-g7eed8d8-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.48.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.48.0-1) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.11-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.7-2_armhf.deb ...
Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
Unpacking libarchive-zip-perl (1.57-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.016-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
Unpacking libtool (2.4.6-0.1) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../dh-autoreconf_12_all.deb ...
Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../debhelper_9.20160403_all.deb ...
Unpacking debhelper (9.20160403) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../libexpat1-dev_2.1.1-1_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.1.1-1) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../libhts-dev_1.3-2+rpi1_armhf.deb ...
Unpacking libhts-dev:armhf (1.3-2+rpi1) ...
Selecting previously unselected package libpython2.7-dev:armhf.
Preparing to unpack .../libpython2.7-dev_2.7.11-7_armhf.deb ...
Unpacking libpython2.7-dev:armhf (2.7.11-7) ...
Selecting previously unselected package libpython-dev:armhf.
Preparing to unpack .../libpython-dev_2.7.11-1_armhf.deb ...
Unpacking libpython-dev:armhf (2.7.11-1) ...
Selecting previously unselected package libpython-all-dev:armhf.
Preparing to unpack .../libpython-all-dev_2.7.11-1_armhf.deb ...
Unpacking libpython-all-dev:armhf (2.7.11-1) ...
Selecting previously unselected package libpython3.5:armhf.
Preparing to unpack .../libpython3.5_3.5.1-5_armhf.deb ...
Unpacking libpython3.5:armhf (3.5.1-5) ...
Selecting previously unselected package libpython3.5-dev:armhf.
Preparing to unpack .../libpython3.5-dev_3.5.1-5_armhf.deb ...
Unpacking libpython3.5-dev:armhf (3.5.1-5) ...
Selecting previously unselected package libpython3-dev:armhf.
Preparing to unpack .../libpython3-dev_3.5.1-3_armhf.deb ...
Unpacking libpython3-dev:armhf (3.5.1-3) ...
Selecting previously unselected package libpython3-all-dev:armhf.
Preparing to unpack .../libpython3-all-dev_3.5.1-3_armhf.deb ...
Unpacking libpython3-all-dev:armhf (3.5.1-3) ...
Selecting previously unselected package python-all.
Preparing to unpack .../python-all_2.7.11-1_armhf.deb ...
Unpacking python-all (2.7.11-1) ...
Selecting previously unselected package python2.7-dev.
Preparing to unpack .../python2.7-dev_2.7.11-7_armhf.deb ...
Unpacking python2.7-dev (2.7.11-7) ...
Selecting previously unselected package python-dev.
Preparing to unpack .../python-dev_2.7.11-1_armhf.deb ...
Unpacking python-dev (2.7.11-1) ...
Selecting previously unselected package python-all-dev.
Preparing to unpack .../python-all-dev_2.7.11-1_armhf.deb ...
Unpacking python-all-dev (2.7.11-1) ...
Selecting previously unselected package python-pkg-resources.
Preparing to unpack .../python-pkg-resources_18.8-1_all.deb ...
Unpacking python-pkg-resources (18.8-1) ...
Selecting previously unselected package python-nose.
Preparing to unpack .../python-nose_1.3.7-1_all.deb ...
Unpacking python-nose (1.3.7-1) ...
Selecting previously unselected package python-setuptools.
Preparing to unpack .../python-setuptools_18.8-1_all.deb ...
Unpacking python-setuptools (18.8-1) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../python3-all_3.5.1-3_armhf.deb ...
Unpacking python3-all (3.5.1-3) ...
Selecting previously unselected package python3.5-dev.
Preparing to unpack .../python3.5-dev_3.5.1-5_armhf.deb ...
Unpacking python3.5-dev (3.5.1-5) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../python3-dev_3.5.1-3_armhf.deb ...
Unpacking python3-dev (3.5.1-3) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../python3-all-dev_3.5.1-3_armhf.deb ...
Unpacking python3-all-dev (3.5.1-3) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../python3-pkg-resources_18.8-1_all.deb ...
Unpacking python3-pkg-resources (18.8-1) ...
Selecting previously unselected package python3-nose.
Preparing to unpack .../python3-nose_1.3.7-1_all.deb ...
Unpacking python3-nose (1.3.7-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../python3-setuptools_18.8-1_all.deb ...
Unpacking python3-setuptools (18.8-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../samtools_1.3-1_armhf.deb ...
Unpacking samtools (1.3-1) ...
Selecting previously unselected package tabix.
Preparing to unpack .../tabix_1.3-2+rpi1_armhf.deb ...
Unpacking tabix (1.3-2+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-python-pysam-dummy.
Preparing to unpack .../sbuild-build-depends-python-pysam-dummy.deb ...
Unpacking sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.11.1-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-7) ...
Setting up python2.7 (2.7.11-7) ...
Setting up libpython-stdlib:armhf (2.7.11-1) ...
Setting up python (2.7.11-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up libpython3.5-stdlib:armhf (3.5.1-5) ...
Setting up python3.5 (3.5.1-5) ...
Setting up libpython3-stdlib:armhf (3.5.1-3) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libpython2.7:armhf (2.7.11-7) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libgsl2:armhf (2.1+dfsg-2) ...
Setting up libhts1:armhf (1.3-2+rpi1) ...
Setting up bcftools (1.3-3) ...
Setting up cython (0.23.4+git4-g7eed8d8-1) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtool (2.4.6-0.1) ...
Setting up libexpat1-dev:armhf (2.1.1-1) ...
Setting up libhts-dev:armhf (1.3-2+rpi1) ...
Setting up libpython2.7-dev:armhf (2.7.11-7) ...
Setting up libpython-dev:armhf (2.7.11-1) ...
Setting up libpython-all-dev:armhf (2.7.11-1) ...
Setting up libpython3.5:armhf (3.5.1-5) ...
Setting up libpython3.5-dev:armhf (3.5.1-5) ...
Setting up libpython3-dev:armhf (3.5.1-3) ...
Setting up libpython3-all-dev:armhf (3.5.1-3) ...
Setting up python-all (2.7.11-1) ...
Setting up python2.7-dev (2.7.11-7) ...
Setting up python-dev (2.7.11-1) ...
Setting up python-all-dev (2.7.11-1) ...
Setting up python-pkg-resources (18.8-1) ...
Setting up python-nose (1.3.7-1) ...
Setting up python-setuptools (18.8-1) ...
Setting up python3.5-dev (3.5.1-5) ...
Setting up samtools (1.3-1) ...
Setting up tabix (1.3-2+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up dh-python (2.20151103) ...
Setting up python3 (3.5.1-3) ...
Setting up cython3 (0.23.4+git4-g7eed8d8-1) ...
Setting up dh-autoreconf (12) ...
Setting up python3-all (3.5.1-3) ...
Setting up python3-dev (3.5.1-3) ...
Setting up python3-all-dev (3.5.1-3) ...
Setting up python3-pkg-resources (18.8-1) ...
Setting up python3-nose (1.3.7-1) ...
Setting up python3-setuptools (18.8-1) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.114 apt_1.2.6 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 bcftools_1.3-3 binutils_2.26-5 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 cython_0.23.4+git4-g7eed8d8-1 cython3_0.23.4+git4-g7eed8d8-1 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-python_2.20151103 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.57-1 libasan1_4.9.3-12 libasan2_5.3.1-11 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libexpat1_2.1.1-1 libexpat1-dev_2.1.1-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-12 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libgsl2_2.1+dfsg-2 libhts-dev_1.3-2+rpi1 libhts1_1.3-2+rpi1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libpython-all-dev_2.7.11-1 libpython-dev_2.7.11-1 libpython-stdlib_2.7.11-1 libpython2.7_2.7.11-7 libpython2.7-dev_2.7.11-7 libpython2.7-minimal_2.7.11-7 libpython2.7-stdlib_2.7.11-7 libpython3-all-dev_3.5.1-3 libpython3-dev_3.5.1-3 libpython3-stdlib_3.5.1-3 libpython3.5_3.5.1-5 libpython3.5-dev_3.5.1-5 libpython3.5-minimal_3.5.1-5 libpython3.5-stdlib_3.5.1-5 libreadline6_6.3-8+b3 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-6 libsqlite3-0_3.11.1-1 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsystemd0_229-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libtool_2.4.6-0.1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 python_2.7.11-1 python-all_2.7.11-1 python-all-dev_2.7.11-1 python-dev_2.7.11-1 python-minimal_2.7.11-1 python-nose_1.3.7-1 python-pkg-resources_18.8-1 python-setuptools_18.8-1 python2.7_2.7.11-7 python2.7-dev_2.7.11-7 python2.7-minimal_2.7.11-7 python3_3.5.1-3 python3-all_3.5.1-3 python3-all-dev_3.5.1-3 python3-dev_3.5.1-3 python3-minimal_3.5.1-3 python3-nose_1.3.7-1 python3-pkg-resources_18.8-1 python3-setuptools_18.8-1 python3.5_3.5.1-5 python3.5-dev_3.5.1-5 python3.5-minimal_3.5.1-5 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_1.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tabix_1.3-2+rpi1 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu Mar 10 07:48:01 2016 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./python-pysam_0.9.0+ds-1.dsc
dpkg-source: info: extracting python-pysam in python-pysam-0.9.0+ds
dpkg-source: info: unpacking python-pysam_0.9.0+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.9.0+ds-1.debian.tar.xz
dpkg-source: info: applying external-htslib.patch
dpkg-source: info: applying disable-tests-requiring-network.patch
dpkg-source: info: applying rpath.patch
dpkg-source: info: applying compile-test.patch

Check disc space
----------------

Sufficient free space for build

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

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-215c4778-93f5-4a43-b8cc-e1b783f6fdf3
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: source package python-pysam
dpkg-buildpackage: source version 0.9.0+ds-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build python-pysam-0.9.0+ds
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
/usr/bin/make -C tests/pysam_data clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c
LC_ALL=C.UTF-8 dh clean --with python2,python3 --buildsystem=pybuild
   dh_testdir -O--buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
dh_auto_clean
I: pybuild base:184: python2.7 setup.py clean 
# pysam: htslib mode is external
running clean
removing '/<<BUILDDIR>>/python-pysam-0.9.0+ds/.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
I: pybuild base:184: python3.5 setup.py clean 
# pysam: htslib mode is external
running clean
removing '/<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.5' does not exist -- can't clean it
rm -f \
	pysam/config.py \
	pysam/config.h
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
LC_ALL=C.UTF-8 dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_testdir -a -O--buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
dh_auto_configure
I: pybuild base:184: python2.7 setup.py config 
# pysam: htslib mode is external
running config
I: pybuild base:184: python3.5 setup.py config 
# pysam: htslib mode is external
running config
touch samtools/config.h
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build 
# pysam: htslib mode is external
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/calignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/calignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/chtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/ctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/ctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cutils.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/chtslib.c -o build/temp.linux-armv7l-2.7/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/chtslib.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
creating build/temp.linux-armv7l-2.7/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/csamfile.c -o build/temp.linux-armv7l-2.7/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
warning: pysam/calignmentfile.pyx:420:12: Unreachable code
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/calignmentfile.c -o build/temp.linux-armv7l-2.7/pysam/calignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:23238:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignmentfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so
cythoning pysam/calignedsegment.pyx to pysam/calignedsegment.c
building 'pysam.calignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/calignedsegment.c -o build/temp.linux-armv7l-2.7/pysam/calignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignedsegment.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.so
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-armv7l-2.7/pysam/ctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:6026:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10644:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabix.o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
warning: pysam/cvcf.pyx:1072:27: Unreachable code
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-armv7l-2.7/pysam/cvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21604:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:17024:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cvcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cbcf.c -o build/temp.linux-armv7l-2.7/pysam/cbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cfaidx.c -o build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
creating build/temp.linux-armv7l-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cutils.c -o build/temp.linux-armv7l-2.7/pysam/cutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cutils.c: In function ‘__pyx_pf_5pysam_6cutils_11_pysam_dispatch’:
pysam/cutils.c:6005:40: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c:6034:40: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c: In function ‘__pyx_pw_5pysam_6cutils_12_pysam_dispatch’:
pysam/cutils.c:10938:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^
pysam/cutils.c:5341:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armv7l-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cutils.o build/temp.linux-armv7l-2.7/pysam/pysam_util.o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-2.7/samtools/dict.c.pysam.o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/convert.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/em.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/filter.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/main.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/version.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so
I: pybuild base:184: /usr/bin/python3 setup.py build 
# pysam: htslib mode is external
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/calignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/calignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/chtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/csamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/ctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/ctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cutils.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
creating build/temp.linux-armv7l-3.5
creating build/temp.linux-armv7l-3.5/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.5/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/chtslib.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
creating build/temp.linux-armv7l-3.5/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.5/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.5/pysam/calignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:23238:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignmentfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
building 'pysam.calignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/calignedsegment.c -o build/temp.linux-armv7l-3.5/pysam/calignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignedsegment.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.5/pysam/ctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:6026:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10644:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabix.o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.5/pysam/cvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21604:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:17024:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cvcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.5/pysam/cbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cbcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
creating build/temp.linux-armv7l-3.5/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cutils.c -o build/temp.linux-armv7l-3.5/pysam/cutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cutils.c: In function ‘__pyx_pf_5pysam_6cutils_11_pysam_dispatch’:
pysam/cutils.c:6005:40: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c:6034:40: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c: In function ‘__pyx_pw_5pysam_6cutils_12_pysam_dispatch’:
pysam/cutils.c:137:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^
pysam/cutils.c:5341:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.5/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cutils.o build/temp.linux-armv7l-3.5/pysam/pysam_util.o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.5/samtools/dict.c.pysam.o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/convert.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/em.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/filter.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/main.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/version.c.pysam.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so
warning: pysam/calignmentfile.pyx:420:12: Unreachable code
warning: pysam/cvcf.pyx:1072:27: Unreachable code
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
cd tests && make -C pysam_data
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS test_query_position.sam > test_query_position.bam
touch tmp.list
samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam
rm -f tmp.list
samtools view -bS ex6.sam > ex6.bam
samtools view -bS example_user_header.sam > example_user_header.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index ex4.bam
samtools index rg_with_tab.bam
samtools index ex9_nofail.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex6.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
cd tests/cbcf_data && make
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz    # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz  # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz    # create tbi index
bcftools index example_vcf40.vcf.gz  # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz    # create tbi index
bcftools index missing_genotypes.vcf.gz  # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz    # create tbi index
bcftools index example_vcf42.vcf.gz  # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz    # create tbi index
bcftools index example_vcf42_only_header.vcf.gz  # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/cbcf_data'
# dh_auto_test	# unfortunately this does not work out of the box
# see https://lists.debian.org/debian-python/2015/07/msg00064.html
# thus trying manually with unusual tricks
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd tests && if [ {version} = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi" dh_auto_test || \
	echo "Ignoring test failures"
I: pybuild base:184: cd tests && if [ 2.7 = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi
.........................................................................................Segmentation fault
E: pybuild pybuild:274: test: plugin custom failed with: exit code=139: cd tests && if [ 2.7 = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi
dh_auto_test: pybuild --test -i python{version} -p 2.7 --dir . returned exit code 13
Ignoring test failures
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
 fakeroot debian/rules binary-arch
LC_ALL=C.UTF-8 dh binary-arch --with python2,python3 --buildsystem=pybuild
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
   dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py install --root /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam 
# pysam: htslib mode is external
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
running build_ext
skipping 'pysam/chtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/chtslib.c -o build/temp.linux-armv7l-2.7/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/chtslib.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so
skipping 'pysam/csamfile.c' Cython extension (up-to-date)
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/csamfile.c -o build/temp.linux-armv7l-2.7/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so
skipping 'pysam/calignmentfile.c' Cython extension (up-to-date)
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/calignmentfile.c -o build/temp.linux-armv7l-2.7/pysam/calignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:23238:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignmentfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/ctabix.c' Cython extension (up-to-date)
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-armv7l-2.7/pysam/ctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:6026:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10644:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabix.o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so
skipping 'pysam/ctabixproxies.c' Cython extension (up-to-date)
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so
skipping 'pysam/cvcf.c' Cython extension (up-to-date)
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-armv7l-2.7/pysam/cvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21604:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:17024:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cvcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so
skipping 'pysam/cbcf.c' Cython extension (up-to-date)
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cbcf.c -o build/temp.linux-armv7l-2.7/pysam/cbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so
skipping 'pysam/cfaidx.c' Cython extension (up-to-date)
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cfaidx.c -o build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so
skipping 'pysam/cutils.c' Cython extension (up-to-date)
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/cutils.c -o build/temp.linux-armv7l-2.7/pysam/cutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cutils.c: In function ‘__pyx_pf_5pysam_6cutils_11_pysam_dispatch’:
pysam/cutils.c:6005:40: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c:6034:40: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c: In function ‘__pyx_pw_5pysam_6cutils_12_pysam_dispatch’:
pysam/cutils.c:10938:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^
pysam/cutils.c:5341:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armv7l-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cutils.o build/temp.linux-armv7l-2.7/pysam/pysam_util.o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-2.7/samtools/dict.c.pysam.o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/convert.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/em.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/filter.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/main.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-2.7/bcftools/version.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/chtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/utils.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/samtools.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.pyc -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/namedtuple.py to namedtuple.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc
running install_egg_info
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:184: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam 
# pysam: htslib mode is external
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
Fixing /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.5/pysam/chtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/chtslib.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.5/pysam/csamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.5/pysam/calignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:23238:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignmentfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.5/pysam/ctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:6026:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10644:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabix.o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.5/pysam/cvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21604:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:17024:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cvcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.5/pysam/cbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cbcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/cutils.c -o build/temp.linux-armv7l-3.5/pysam/cutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/cutils.c: In function ‘__pyx_pf_5pysam_6cutils_11_pysam_dispatch’:
pysam/cutils.c:6005:40: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c:6034:40: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
                       __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                                        ^
pysam/cutils.c: In function ‘__pyx_pw_5pysam_6cutils_12_pysam_dispatch’:
pysam/cutils.c:137:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^
pysam/cutils.c:5341:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.5/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-armv7l-3.5/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cutils.o build/temp.linux-armv7l-3.5/pysam/pysam_util.o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamtk.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.5/samtools/dict.c.pysam.o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/HMM.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/ccall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/consensus.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/convert.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/em.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/filter.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/kmin.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/main.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/mcall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/prob1.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/tabix.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-armv7l-3.5/bcftools/version.c.pysam.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
creating /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/chtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.9.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/Pileup.py to Pileup.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__init__.py to __init__.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/bcftools.py to bcftools.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/namedtuple.py to namedtuple.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/samtools.py to samtools.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/utils.py to utils.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/version.py to version.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/__init__.py to __init__.cpython-35.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/config.py to config.cpython-35.pyc
running install_egg_info
running egg_info
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
writing pysam.egg-info/PKG-INFO
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: pysam/calignmentfile.pyx:420:12: Unreachable code
warning: pysam/cvcf.pyx:1072:27: Unreachable code
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.9.0+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam-0.9.0.egg-info
Skipping SOURCES.txt
running install_scripts
   debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
/usr/bin/make -C tests/pysam_data clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds/tests/pysam_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c
dh_install -Xtest.gtf.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.9.0+ds'
   dh_installdocs -a -O--buildsystem=pybuild
   dh_installchangelogs -a -O--buildsystem=pybuild
   dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:328: renaming calignedsegment.so to calignedsegment.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming calignmentfile.so to calignmentfile.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cbcf.so to cbcf.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cfaidx.so to cfaidx.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming csamfile.so to csamfile.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming ctabix.so to ctabix.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming ctabixproxies.so to ctabixproxies.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cutils.so to cutils.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cvcf.so to cvcf.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming libchtslib.so to libchtslib.arm-linux-gnueabihf.so
   dh_python3 -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
   dh_fixperms -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -a -O--buildsystem=pybuild
   dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions}
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions}
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions}
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides}
   dh_md5sums -a -O--buildsystem=pybuild
   dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-pysam-dbgsym' in '../python-pysam-dbgsym_0.9.0+ds-1_armhf.deb'.
dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.9.0+ds-1_armhf.deb'.
dpkg-deb: building package 'python-pysam' in '../python-pysam_0.9.0+ds-1_armhf.deb'.
dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.9.0+ds-1_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pysam_0.9.0+ds-1_armhf.changes
dpkg-genchanges: warning: package python3-pysam-dbgsym listed in files list but not in control info
dpkg-genchanges: warning: package python-pysam-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build python-pysam-0.9.0+ds
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160410-0346

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


python-pysam_0.9.0+ds-1_armhf.changes:
--------------------------------------

Format: 1.8
Date: Wed, 09 Mar 2016 23:43:59 -0800
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: armhf
Version: 0.9.0+ds-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format (
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Closes: 814765
Changes:
 python-pysam (0.9.0+ds-1) unstable; urgency=medium
 .
   * Add filenamemangle to d/watch and space out content
   * Imported Upstream version 0.9.0+ds (Closes: #814765)
   * Bump htslib and samtools minimum versions
   * Update policy statndards-version to 3.9.7
   * Use encrypted protocols for Vcs URLs in d/control
   * Use readthedocs page as pysam's homepage
   * Update packaging for external htslib link
   * Refresh patches
   * Delete obsolete patch
Checksums-Sha1:
 0d10c6f14aab91d74d1c803f74e91d4a9974c1f2 2997908 python-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 d424b029f052909cb099a613c9790e2053f6a4ef 936738 python-pysam_0.9.0+ds-1_armhf.deb
 fafc5a65bbb8139faaa80b94905302422fcfbf72 3299202 python3-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 f96055b188ad1205ed3019a021faf67b0d4db043 935994 python3-pysam_0.9.0+ds-1_armhf.deb
Checksums-Sha256:
 99e4c62b62b10366f66521c1bdc1cd16b728f7f4864929916a05d4e2b5315b06 2997908 python-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 f6f5233b71046cebb3cbc7b520ed035b923c1affe62c88083b06c463e9d445e4 936738 python-pysam_0.9.0+ds-1_armhf.deb
 f26f099e4db344fd2466c35f9cd250878c7b189ce1b69d8b65be2f016144182f 3299202 python3-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 9ddae1a539ff4a42489db9b14b81774ef0fc18a435c2d8ef52a5a9171c8b3a6c 935994 python3-pysam_0.9.0+ds-1_armhf.deb
Files:
 b511529c56dd00f5272183d61916e936 2997908 debug extra python-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 e9d1a922adb5b4de6e3a62795e0c4719 936738 python optional python-pysam_0.9.0+ds-1_armhf.deb
 37f3e914b7f44b090e8a40b5e10cddcc 3299202 debug extra python3-pysam-dbgsym_0.9.0+ds-1_armhf.deb
 98483b735d189d4925e0fe9aa9956445 935994 python optional python3-pysam_0.9.0+ds-1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


python-pysam-dbgsym_0.9.0+ds-1_armhf.deb
----------------------------------------

 new debian package, version 2.0.
 size 2997908 bytes: control archive=996 bytes.
     812 bytes,    13 lines      control              
    1060 bytes,    10 lines      md5sums              
 Package: python-pysam-dbgsym
 Source: python-pysam
 Version: 0.9.0+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3412
 Depends: python-pysam (= 0.9.0+ds-1)
 Section: debug
 Priority: extra
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: Debug symbols for python-pysam
 Auto-Built-Package: debug-symbols
 Build-Ids: 189e25cf637bb4b42a83251e1fda52c25b9e89ea 2093a8dcb21d35bbc01aec76df6ed47d5db9275e 28df6b5f5650e4319a68eb97d4f76dfb64e3ad0d 4593d7caa59330fdb8fefb418b09296a693d7070 55733a5e7b84df60397f34ed1f65206c1b02998d 9cffc058050ac024c42f55a8dbd6dba8f65abcb8 a191c0c0d6b60c96d157d8fb57551ae3944c095f b52907c32640c7a0dcaabecd31c6be286f206bcb b659a9fc87991f78745c8950de20bd247f1fb443 c5046bf41ccd86508f660738f443fd3c3e06e023

drwxr-xr-x root/root         0 2016-04-10 03:45 ./
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/18/
-rw-r--r-- root/root     41844 2016-04-10 03:45 ./usr/lib/debug/.build-id/18/9e25cf637bb4b42a83251e1fda52c25b9e89ea.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/20/
-rw-r--r-- root/root    372240 2016-04-10 03:45 ./usr/lib/debug/.build-id/20/93a8dcb21d35bbc01aec76df6ed47d5db9275e.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/28/
-rw-r--r-- root/root    453676 2016-04-10 03:45 ./usr/lib/debug/.build-id/28/df6b5f5650e4319a68eb97d4f76dfb64e3ad0d.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root    378040 2016-04-10 03:45 ./usr/lib/debug/.build-id/45/93d7caa59330fdb8fefb418b09296a693d7070.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/55/
-rw-r--r-- root/root    153812 2016-04-10 03:45 ./usr/lib/debug/.build-id/55/733a5e7b84df60397f34ed1f65206c1b02998d.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root    167136 2016-04-10 03:45 ./usr/lib/debug/.build-id/9c/ffc058050ac024c42f55a8dbd6dba8f65abcb8.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root    654696 2016-04-10 03:45 ./usr/lib/debug/.build-id/a1/91c0c0d6b60c96d157d8fb57551ae3944c095f.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/b5/
-rw-r--r-- root/root     24976 2016-04-10 03:45 ./usr/lib/debug/.build-id/b5/2907c32640c7a0dcaabecd31c6be286f206bcb.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/b6/
-rw-r--r-- root/root   1032844 2016-04-10 03:45 ./usr/lib/debug/.build-id/b6/59a9fc87991f78745c8950de20bd247f1fb443.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root    188916 2016-04-10 03:45 ./usr/lib/debug/.build-id/c5/046bf41ccd86508f660738f443fd3c3e06e023.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/share/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/share/doc/
lrwxrwxrwx root/root         0 2016-04-10 03:45 ./usr/share/doc/python-pysam-dbgsym -> python-pysam


python-pysam_0.9.0+ds-1_armhf.deb
---------------------------------

 new debian package, version 2.0.
 size 936738 bytes: control archive=3065 bytes.
     678 bytes,    15 lines      control              
    7260 bytes,    77 lines      md5sums              
     160 bytes,     9 lines   *  postinst             #!/bin/sh
     259 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-pysam
 Version: 0.9.0+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3460
 Depends: libc6 (>= 2.7), libhts1 (>= 1.3), zlib1g (>= 1:1.2.3.3), python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~)
 Section: python
 Priority: optional
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 2.

drwxr-xr-x root/root         0 2016-04-10 03:45 ./
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info/
-rw-r--r-- root/root      1139 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info/dependency_links.txt
-rw-r--r-- root/root         1 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info/not-zip-safe
-rw-r--r-- root/root         6 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam-0.9.0.egg-info/top_level.txt
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/
-rw-r--r-- root/root      8305 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/Pileup.py
-rw-r--r-- root/root      3185 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/__init__.py
-rw-r--r-- root/root       428 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/bcftools.py
-rw-r--r-- root/root    292152 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/calignedsegment.arm-linux-gnueabihf.so
-rw-r--r-- root/root      2971 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/calignedsegment.pxd
-rw-r--r-- root/root    338016 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/calignmentfile.arm-linux-gnueabihf.so
-rw-r--r-- root/root      3986 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/calignmentfile.pxd
-rw-r--r-- root/root    522096 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/cbcf.arm-linux-gnueabihf.so
-rw-r--r-- root/root      4968 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/cbcf.pxd
-rw-r--r-- root/root    128940 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/cfaidx.arm-linux-gnueabihf.so
-rw-r--r-- root/root      2142 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/cfaidx.pxd
-rw-r--r-- root/root     79955 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/chtslib.pxd
-rw-r--r-- root/root        16 2016-04-10 03:12 ./usr/lib/python2.7/dist-packages/pysam/config.py
-rw-r--r-- root/root     31300 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/csamfile.arm-linux-gnueabihf.so
-rw-r--r-- root/root      1505 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/csamfile.pxd
-rw-r--r-- root/root    167928 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/ctabix.arm-linux-gnueabihf.so
-rw-r--r-- root/root      2787 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/ctabix.pxd
-rw-r--r-- root/root    135244 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/ctabixproxies.arm-linux-gnueabihf.so
-rw-r--r-- root/root      1320 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/ctabixproxies.pxd
-rw-r--r-- root/root    982656 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/cutils.arm-linux-gnueabihf.so
-rw-r--r-- root/root      1505 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/cutils.pxd
-rw-r--r-- root/root    507748 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/cvcf.arm-linux-gnueabihf.so
-rw-r--r-- root/root         2 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/cvcf.pxd
-rw-r--r-- root/root      3697 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/htslib_util.h
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python2.7/dist-packages/pysam/include/
-rw-r--r-- root/root         0 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/__init__.py
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/
-rw-r--r-- root/root      4180 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/HMM.h
-rw-r--r-- root/root      2345 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/bcftools.h
-rw-r--r-- root/root      4595 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/call.h
-rw-r--r-- root/root      1730 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/convert.h
-rw-r--r-- root/root      1982 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/filter.h
-rw-r--r-- root/root      1561 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/gvcf.h
-rw-r--r-- root/root      2724 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/khash_str2str.h
-rw-r--r-- root/root      1619 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/kmin.h
-rw-r--r-- root/root      4416 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/ploidy.h
-rw-r--r-- root/root      3539 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/prob1.h
-rw-r--r-- root/root        82 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/pysam.h
-rw-r--r-- root/root      5851 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/rbuf.h
-rw-r--r-- root/root      2621 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/tsv2vcf.h
-rw-r--r-- root/root      2387 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/vcmp.h
-rw-r--r-- root/root        31 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/bcftools/version.h
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/
-rw-r--r-- root/root     20927 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam.h
-rw-r--r-- root/root      5126 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam2bcf.h
-rw-r--r-- root/root      2273 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_endian.h
-rw-r--r-- root/root      2058 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_lpileup.h
-rw-r--r-- root/root      1842 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_plbuf.h
-rw-r--r-- root/root      3421 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/bam_tview.h
-rw-r--r-- root/root         0 2016-04-10 02:35 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/config.h
-rw-r--r-- root/root      1656 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/errmod.h
-rw-r--r-- root/root      1567 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/kprobaln.h
-rw-r--r-- root/root        82 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/pysam.h
-rw-r--r-- root/root      5317 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/sam.h
-rw-r--r-- root/root      2796 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/sam_header.h
-rw-r--r-- root/root      3879 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/sam_opts.h
-rw-r--r-- root/root      1560 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/sample.h
-rw-r--r-- root/root      1581 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/samtools.h
-rw-r--r-- root/root      2484 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/stats_isize.h
-rw-r--r-- root/root        31 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/version.h
drwxr-xr-x root/root         0 2016-04-10 03:27 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/win32/
-rw-r--r-- root/root     49915 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/win32/xcurses.h
-rw-r--r-- root/root      9544 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/win32/zconf.h
-rw-r--r-- root/root     66188 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/include/samtools/win32/zlib.h
-rw-r--r-- root/root     14232 2016-04-10 03:45 ./usr/lib/python2.7/dist-packages/pysam/libchtslib.arm-linux-gnueabihf.so
-rw-r--r-- root/root      5056 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/namedtuple.py
-rw-r--r-- root/root       223 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/pysam_stream.h
-rw-r--r-- root/root       538 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/pysam_util.h
-rw-r--r-- root/root       180 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/samfile_util.h
-rw-r--r-- root/root      1416 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/samtools.py
-rw-r--r-- root/root       218 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/tabix_util.h
-rw-r--r-- root/root      2655 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/utils.py
-rw-r--r-- root/root       112 2016-03-01 22:40 ./usr/lib/python2.7/dist-packages/pysam/version.py
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/doc/python-pysam/
-rw-r--r-- root/root       219 2016-03-10 07:34 ./usr/share/doc/python-pysam/TODO.Debian
-rw-r--r-- root/root      1821 2016-03-10 07:44 ./usr/share/doc/python-pysam/changelog.Debian.gz
-rw-r--r-- root/root      6835 2016-03-06 06:31 ./usr/share/doc/python-pysam/copyright
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/lintian/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       643 2015-11-27 19:52 ./usr/share/lintian/overrides/python-pysam


python3-pysam-dbgsym_0.9.0+ds-1_armhf.deb
-----------------------------------------

 new debian package, version 2.0.
 size 3299202 bytes: control archive=997 bytes.
     815 bytes,    13 lines      control              
    1060 bytes,    10 lines      md5sums              
 Package: python3-pysam-dbgsym
 Source: python-pysam
 Version: 0.9.0+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3708
 Depends: python3-pysam (= 0.9.0+ds-1)
 Section: debug
 Priority: extra
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: Debug symbols for python3-pysam
 Auto-Built-Package: debug-symbols
 Build-Ids: 1beea3f0dbd4ae91825417ce50ae0c3678f8be7f 485691b7153ca5989e76067dfdc4dc0348fffb9b 4a288dbe9252abad48359f373f80152aec2879d7 6129b478c62222415f2fc39bf6d8b4ae7af95258 99021ea259a375a6e5aadaef307249e64f6f5eb5 ae5bd68f1d23a2f1978f512b7caaa339d3d9e067 b90b2d9e0d45b4479b4e47a5d24a61c84e92fe22 d9f03e395c6d12669e2c7d8b6b5d3801d2a1f174 ea2f08ced0e9b6d478075eb92a4012e47c473606 f9683cb7b95bd68164af51272d234bcf75848432

drwxr-xr-x root/root         0 2016-04-10 03:45 ./
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/1b/
-rw-r--r-- root/root   1058452 2016-04-10 03:45 ./usr/lib/debug/.build-id/1b/eea3f0dbd4ae91825417ce50ae0c3678f8be7f.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root    716540 2016-04-10 03:45 ./usr/lib/debug/.build-id/48/5691b7153ca5989e76067dfdc4dc0348fffb9b.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/4a/
-rw-r--r-- root/root    415016 2016-04-10 03:45 ./usr/lib/debug/.build-id/4a/288dbe9252abad48359f373f80152aec2879d7.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root    189856 2016-04-10 03:45 ./usr/lib/debug/.build-id/61/29b478c62222415f2fc39bf6d8b4ae7af95258.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root    417800 2016-04-10 03:45 ./usr/lib/debug/.build-id/99/021ea259a375a6e5aadaef307249e64f6f5eb5.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/ae/
-rw-r--r-- root/root     25744 2016-04-10 03:45 ./usr/lib/debug/.build-id/ae/5bd68f1d23a2f1978f512b7caaa339d3d9e067.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root    206236 2016-04-10 03:45 ./usr/lib/debug/.build-id/b9/0b2d9e0d45b4479b4e47a5d24a61c84e92fe22.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/d9/
-rw-r--r-- root/root    166416 2016-04-10 03:45 ./usr/lib/debug/.build-id/d9/f03e395c6d12669e2c7d8b6b5d3801d2a1f174.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/ea/
-rw-r--r-- root/root     43656 2016-04-10 03:45 ./usr/lib/debug/.build-id/ea/2f08ced0e9b6d478075eb92a4012e47c473606.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/debug/.build-id/f9/
-rw-r--r-- root/root    531868 2016-04-10 03:45 ./usr/lib/debug/.build-id/f9/683cb7b95bd68164af51272d234bcf75848432.debug
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/share/
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/share/doc/
lrwxrwxrwx root/root         0 2016-04-10 03:45 ./usr/share/doc/python3-pysam-dbgsym -> python3-pysam


python3-pysam_0.9.0+ds-1_armhf.deb
----------------------------------

 new debian package, version 2.0.
 size 935994 bytes: control archive=3142 bytes.
     676 bytes,    16 lines      control              
    7164 bytes,    76 lines      md5sums              
     170 bytes,     9 lines   *  postinst             #!/bin/sh
     399 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-pysam
 Source: python-pysam
 Version: 0.9.0+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3426
 Depends: libc6 (>= 2.7), libhts1 (>= 1.3), zlib1g (>= 1:1.2.3.3), python3 (<< 3.6), python3 (>= 3.5~)
 Section: python
 Priority: optional
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 3.

drwxr-xr-x root/root         0 2016-04-10 03:45 ./
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam-0.9.0.egg-info/
-rw-r--r-- root/root      1139 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam-0.9.0.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam-0.9.0.egg-info/dependency_links.txt
-rw-r--r-- root/root         1 2016-04-10 03:27 ./usr/lib/python3/dist-packages/pysam-0.9.0.egg-info/not-zip-safe
-rw-r--r-- root/root         6 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam-0.9.0.egg-info/top_level.txt
drwxr-xr-x root/root         0 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/
-rw-r--r-- root/root      8305 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/Pileup.py
-rw-r--r-- root/root      3185 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/__init__.py
-rw-r--r-- root/root       429 2016-04-10 02:53 ./usr/lib/python3/dist-packages/pysam/bcftools.py
-rw-r--r-- root/root    292248 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/calignedsegment.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      2971 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/calignedsegment.pxd
-rw-r--r-- root/root    325840 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      3986 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/calignmentfile.pxd
-rw-r--r-- root/root    510012 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      4968 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/cbcf.pxd
-rw-r--r-- root/root    124940 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      2142 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/cfaidx.pxd
-rw-r--r-- root/root     79955 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/chtslib.pxd
-rw-r--r-- root/root        16 2016-04-10 03:27 ./usr/lib/python3/dist-packages/pysam/config.py
-rw-r--r-- root/root     31384 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      1505 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/csamfile.pxd
-rw-r--r-- root/root    168080 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      2787 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/ctabix.pxd
-rw-r--r-- root/root    131224 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      1320 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/ctabixproxies.pxd
-rw-r--r-- root/root    982736 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      1505 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/cutils.pxd
-rw-r--r-- root/root    503804 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root         2 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/cvcf.pxd
-rw-r--r-- root/root      3697 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/htslib_util.h
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam/include/
-rw-r--r-- root/root         0 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/__init__.py
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam/include/bcftools/
-rw-r--r-- root/root      4180 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/HMM.h
-rw-r--r-- root/root      2345 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.h
-rw-r--r-- root/root      4595 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/call.h
-rw-r--r-- root/root      1730 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/convert.h
-rw-r--r-- root/root      1982 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/filter.h
-rw-r--r-- root/root      1561 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/gvcf.h
-rw-r--r-- root/root      2724 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/khash_str2str.h
-rw-r--r-- root/root      1619 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.h
-rw-r--r-- root/root      4416 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ploidy.h
-rw-r--r-- root/root      3539 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/prob1.h
-rw-r--r-- root/root        82 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/pysam.h
-rw-r--r-- root/root      5851 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/rbuf.h
-rw-r--r-- root/root      2621 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/tsv2vcf.h
-rw-r--r-- root/root      2387 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/vcmp.h
-rw-r--r-- root/root        31 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/bcftools/version.h
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam/include/samtools/
-rw-r--r-- root/root     20927 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam.h
-rw-r--r-- root/root      5126 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam2bcf.h
-rw-r--r-- root/root      2273 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_endian.h
-rw-r--r-- root/root      2058 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_lpileup.h
-rw-r--r-- root/root      1842 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_plbuf.h
-rw-r--r-- root/root      3421 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_tview.h
-rw-r--r-- root/root         0 2016-04-10 02:35 ./usr/lib/python3/dist-packages/pysam/include/samtools/config.h
-rw-r--r-- root/root      1656 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/errmod.h
-rw-r--r-- root/root      1567 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/kprobaln.h
-rw-r--r-- root/root        82 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/pysam.h
-rw-r--r-- root/root      5317 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/sam.h
-rw-r--r-- root/root      2796 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/sam_header.h
-rw-r--r-- root/root      3879 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/sam_opts.h
-rw-r--r-- root/root      1560 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/sample.h
-rw-r--r-- root/root      1581 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/samtools.h
-rw-r--r-- root/root      2484 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/stats_isize.h
-rw-r--r-- root/root        31 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/version.h
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/lib/python3/dist-packages/pysam/include/samtools/win32/
-rw-r--r-- root/root     49915 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/win32/xcurses.h
-rw-r--r-- root/root      9544 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/win32/zconf.h
-rw-r--r-- root/root     66188 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/include/samtools/win32/zlib.h
-rw-r--r-- root/root     14296 2016-04-10 03:45 ./usr/lib/python3/dist-packages/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
-rw-r--r-- root/root      5051 2016-04-10 02:53 ./usr/lib/python3/dist-packages/pysam/namedtuple.py
-rw-r--r-- root/root       223 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/pysam_stream.h
-rw-r--r-- root/root       538 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/pysam_util.h
-rw-r--r-- root/root       180 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/samfile_util.h
-rw-r--r-- root/root      1423 2016-04-10 02:53 ./usr/lib/python3/dist-packages/pysam/samtools.py
-rw-r--r-- root/root       218 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/tabix_util.h
-rw-r--r-- root/root      2655 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/utils.py
-rw-r--r-- root/root       112 2016-03-01 22:40 ./usr/lib/python3/dist-packages/pysam/version.py
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/doc/python3-pysam/
-rw-r--r-- root/root      1821 2016-03-10 07:44 ./usr/share/doc/python3-pysam/changelog.Debian.gz
-rw-r--r-- root/root      6835 2016-03-06 06:31 ./usr/share/doc/python3-pysam/copyright
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/lintian/
drwxr-xr-x root/root         0 2016-04-10 03:44 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       587 2015-11-27 19:52 ./usr/share/lintian/overrides/python3-pysam


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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

Build Architecture: armhf
Build-Space: 103408
Build-Time: 4279
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 495
Job: python-pysam_0.9.0+ds-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 4816
Source-Version: 0.9.0+ds-1
Space: 103408
Status: successful
Version: 0.9.0+ds-1
--------------------------------------------------------------------------------
Finished at 20160410-0346
Build needed 01:20:16, 103408k disc space