Raspbian Package Auto-Building

Build log for python-pysam (0.11.2.2+ds-3) on armhf

python-pysam0.11.2.2+ds-3armhf → 2017-10-03 03:49:15

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| python-pysam 0.11.2.2+ds-3 (armhf)           Tue, 03 Oct 2017 03:11:25 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.11.2.2+ds-3
Source Version: 0.11.2.2+ds-3
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-cfbfac07-7246-4c62-9bd7-d6a8607dcdb4' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.4 MB in 8s (2629 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 2487 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main python-pysam 0.11.2.2+ds-3 (dsc) [2609 B]
Get:2 http://172.17.0.1/private buster-staging/main python-pysam 0.11.2.2+ds-3 (tar) [2476 kB]
Get:3 http://172.17.0.1/private buster-staging/main python-pysam 0.11.2.2+ds-3 (diff) [8296 B]
Fetched 2487 kB in 0s (4122 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-n9RaeO/python-pysam-0.11.2.2+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-n9RaeO' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


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

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-oMXa7x/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-oMXa7x/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-oMXa7x/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (7912 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates libreadline5 libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15082 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.4.1), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.4.1), bcftools (>= 1.4.1), python-nose, python3-nose
Filtered Build-Depends: debhelper (>= 10), dh-exec, dh-python, libhts-dev (>= 1.4.1), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.4.1), bcftools (>= 1.4.1), python-nose, python3-nose
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-oMXa7x/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Sources [578 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ Packages [664 B]
Fetched 2575 B in 0s (9664 B/s)
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 packages were automatically installed and are no longer required:
  ca-certificates libreadline5 libsasl2-modules openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgsl23 libgslcblas0
  libgssapi-krb5-2 libhts-dev libhts2 libicu57 libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
  libpipeline1 libpsl5 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 libpython3.6
  libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib librtmp1
  libsigsegv2 libssh2-1 libtimedate-perl libtool 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 python3.6
  python3.6-dev python3.6-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 krb5-doc krb5-user libtool-doc
  gfortran | fortran95-compiler gcj-jdk m4-doc 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 python3.6-venv python3.6-doc
Recommended packages:
  curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgsl23 libgslcblas0
  libgssapi-krb5-2 libhts-dev libhts2 libicu57 libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
  libpipeline1 libpsl5 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 libpython3.6
  libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib librtmp1
  libsigsegv2 libssh2-1 libtimedate-perl libtool 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 python3.6
  python3.6-dev python3.6-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 99 newly installed, 0 to remove and 16 not upgraded.
Need to get 111 MB of archives.
After this operation, 270 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oMXa7x/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.3-1 [67.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython3.5-minimal armhf 3.5.4-2 [572 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python3.5-minimal armhf 3.5.4-2 [1448 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.5.3-3 [35.4 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.5-stdlib armhf 3.5.4-2 [2097 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.5 armhf 3.5.4-2 [241 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.5.3-3 [18.8 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-python all 2.20170125 [86.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.5.3-3 [21.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.2-2 [574 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.2-2 [1213 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-4 [609 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.26.0-1 [72.2 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.18.0-4 [42.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.55.1-1 [262 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf bcftools armhf 1.4.1-3+rpi1+b2 [404 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf cython armhf 0.25.2-2 [1699 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf cython3 armhf 0.25.2-2 [2419 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.0-1 [2650 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.8 [973 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.3-1 [120 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.13-2 [916 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpython2.7-dev armhf 2.7.13-2 [27.6 MB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpython-dev armhf 2.7.13-2 [20.0 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpython-all-dev armhf 2.7.13-2 [958 B]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpython3.5 armhf 3.5.4-2 [1174 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpython3.5-dev armhf 3.5.4-2 [37.0 MB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libpython3-dev armhf 3.5.3-3 [18.9 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.2-2 [2045 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpython3.6 armhf 3.6.2-2 [1212 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libpython3.6-dev armhf 3.6.2-2 [2221 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libpython3-all-dev armhf 3.5.3-3 [970 B]
Get:80 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.13-2 [940 B]
Get:81 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.13-2 [276 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.13-2 [1130 B]
Get:83 http://172.17.0.1/private buster-staging/main armhf python-all-dev armhf 2.7.13-2 [962 B]
Get:84 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 36.2.7-2 [169 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf python-nose all 1.3.7-2 [132 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 36.2.7-2 [302 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.2-2 [211 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf python3-all armhf 3.5.3-3 [944 B]
Get:89 http://172.17.0.1/private buster-staging/main armhf python3.5-dev armhf 3.5.4-2 [430 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf python3-dev armhf 3.5.3-3 [1158 B]
Get:91 http://172.17.0.1/private buster-staging/main armhf python3.6-dev armhf 3.6.2-2 [501 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf python3-all-dev armhf 3.5.3-3 [972 B]
Get:93 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 36.2.7-2 [140 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf python3-nose all 1.3.7-2 [132 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 36.2.7-2 [220 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.4.1-1 [218 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.4.1-5 [249 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
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Setting up python2.7-dev (2.7.13-2) ...
Setting up python (2.7.13-2) ...
Setting up libpython3.6:armhf (3.6.2-2) ...
Setting up libtool (2.4.6-2) ...
Setting up python3.5 (3.5.4-2) ...
Setting up libpython3-stdlib:armhf (3.5.3-3) ...
Setting up libpython-dev:armhf (2.7.13-2) ...
Setting up libk5crypto3:armhf (1.15.1-2) ...
Setting up python3.6 (3.6.2-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libpython3.5:armhf (3.5.4-2) ...
Setting up python-dev (2.7.13-2) ...
Setting up libpython-all-dev:armhf (2.7.13-2) ...
Setting up python-pkg-resources (36.2.7-2) ...
Setting up libpython3.6-dev:armhf (3.6.2-2) ...
Setting up libpython3.5-dev:armhf (3.5.4-2) ...
Setting up cython (0.25.2-2) ...
Setting up libkrb5-3:armhf (1.15.1-2) ...
Setting up python3.6-dev (3.6.2-2) ...
Setting up python3.5-dev (3.5.4-2) ...
Setting up python-nose (1.3.7-2) ...
Setting up python-all (2.7.13-2) ...
Setting up libpython3-dev:armhf (3.5.3-3) ...
Setting up python-setuptools (36.2.7-2) ...
Setting up libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up python-all-dev (2.7.13-2) ...
Setting up libpython3-all-dev:armhf (3.5.3-3) ...
Setting up libcurl3-gnutls:armhf (7.55.1-1) ...
Setting up tabix (1.4.1-5) ...
Setting up libhts2:armhf (1.4.1-5) ...
Setting up libhts-dev:armhf (1.4.1-5) ...
Setting up samtools (1.4.1-1) ...
Setting up bcftools (1.4.1-3+rpi1+b2) ...
Setting up dh-autoreconf (14) ...
Setting up python3 (3.5.3-3) ...
Setting up python3-dev (3.5.3-3) ...
Setting up python3-pkg-resources (36.2.7-2) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up python3-nose (1.3.7-2) ...
Setting up python3-all (3.5.3-3) ...
Setting up cython3 (0.25.2-2) ...
Setting up python3-setuptools (36.2.7-2) ...
Setting up dh-python (2.20170125) ...
Setting up debhelper (10.8) ...
Setting up python3-all-dev (3.5.3-3) ...
Setting up dh-exec (0.23) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-14) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.29.1-3+rpi1 dpkg-dev_1.18.24 g++-7_7.2.0-5 gcc-7_7.2.0-5 libc6-dev_2.24-14 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch
Package versions: adduser_3.116 apt_1.5 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 bcftools_1.4.1-3+rpi1+b2 binutils_2.29.1-3+rpi1 binutils-arm-linux-gnueabihf_2.29.1-3+rpi1 binutils-common_2.29.1-3+rpi1 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-5 cython_0.25.2-2 cython3_0.25.2-2 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.8 debianutils_4.8.2 dh-autoreconf_14 dh-exec_0.23 dh-python_2.20170125 dh-strip-nondeterminism_0.038-1 diffutils_1:3.6-1 dirmngr_2.2.1-1 dmsetup_2:1.02.142-1 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.6-1 e2fsprogs_1.43.6-1 fakeroot_1.22-1 fdisk_2.29.2-5 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-5 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-7_7.2.0-5 gcc-7-base_7.2.0-5 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-1 gnupg-agent_2.2.1-1 gnupg-l10n_2.2.1-1 gnupg-utils_2.2.1-1 gpg_2.2.1-1 gpg-agent_2.2.1-1 gpg-wks-client_2.2.1-1 gpg-wks-server_2.2.1-1 gpgconf_2.2.1-1 gpgsm_2.2.1-1 gpgv_2.2.1-1 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-11 libapt-pkg5.0_1.5 libarchive-zip-perl_1.59-1 libasan4_7.2.0-5 libassuan0_2.4.3-3 libatomic1_7.2.0-5 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libbinutils_2.29.1-3+rpi1 libblkid1_2.29.2-5 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-14 libc-dev-bin_2.24-14 libc6_2.24-14 libc6-dev_2.24-14 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.2.0-5 libcilkrts5_7.2.0-5 libcomerr2_1.43.6-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.55.1-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.16+really1.10.22-1 libdebconfclient0_0.230 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.18.24 libdrm-common_2.4.82-1+rpi1 libdrm2_2.4.82-1+rpi1 libexpat1_2.2.3-1 libexpat1-dev_2.2.3-1 libfakeroot_1.22-1 libfdisk1_2.29.2-5 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-7-dev_7.2.0-5 libgcc1_1:7.2.0-5 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.0-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.15-2 libgomp1_7.2.0-5 libgpg-error0_1.27-3 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-2 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu57_57.1-6 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.29.2-5 libmpc3_1.0.3-2 libmpdec2_2.4.2-1 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.26.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.0-8 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.32-3 libprocps6_2:3.3.12-3 libpsl5_0.18.0-4 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.5.3-3 libpython3-dev_3.5.3-3 libpython3-stdlib_3.5.3-3 libpython3.5_3.5.4-2 libpython3.5-dev_3.5.4-2 libpython3.5-minimal_3.5.4-2 libpython3.5-stdlib_3.5.4-2 libpython3.6_3.6.2-2 libpython3.6-dev_3.6.2-2 libpython3.6-minimal_3.6.2-2 libpython3.6-stdlib_3.6.2-2 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.29.2-5 libsqlite3-0_3.20.1-1 libss2_1.43.6-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-5 libstdc++6_7.2.0-5 libsystemd0_234-3 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-5 libudev1_234-3 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-5 libxml2_2.9.4+dfsg1-4 linux-base_4.5 linux-libc-dev_4.9.30-2+deb9u2+rpi1+stretch login_1:4.4-4.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-5 mountall_2.54 multiarch-support_2.24-14 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-8 perl-base_5.26.0-8 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-8 pinentry-curses_1.0.0-2 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_36.2.7-2 python-setuptools_36.2.7-2 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-3 python3-all_3.5.3-3 python3-all-dev_3.5.3-3 python3-dev_3.5.3-3 python3-minimal_3.5.3-3 python3-nose_1.3.7-2 python3-pkg-resources_36.2.7-2 python3-setuptools_36.2.7-2 python3.5_3.5.4-2 python3.5-dev_3.5.4-2 python3.5-minimal_3.5.4-2 python3.6_3.6.2-2 python3.6-dev_3.6.2-2 python3.6-minimal_3.6.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.4.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_234-3 sysvinit-utils_2.88dsf-59.10 tabix_1.4.1-5 tar_1.29b-2 tzdata_2017b-2 udev_234-3 util-linux_2.29.2-5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug  1 12:24:05 2017 UTC
gpgv:                using RSA key AFCFEC8E669CE1C2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.11.2.2+ds-3.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.11.2.2+ds
dpkg-source: info: unpacking python-pysam_0.11.2.2+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.11.2.2+ds-3.debian.tar.xz
dpkg-source: info: applying no-usage-test-without-tty.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-cfbfac07-7246-4c62-9bd7-d6a8607dcdb4
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.11.2.2+ds-3
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build python-pysam-0.11.2.2+ds
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+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-0.11.2.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/cbcf_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 \
	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
	tests/pysam_data/ex1.fa.gz \
	tests/pysam_data/ex1.fa.gz.gzi \
	tests/pysam_data/ex1_csi.bam.csi
dh clean --with python2,python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds'
dh_auto_clean
I: pybuild base:184: python2.7 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:184: python3.6 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.6' does not exist -- can't clean it
I: pybuild base:184: python3.5 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it)
'build/bdist.linux-armhf' 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 \
	pysam/lib*.c \
	samtools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:184: python3.6 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:184: python3.5 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+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/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libchtslib.c:4:
pysam/libchtslib.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libchtslib.c:1518:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcsamfile.c:4:
pysam/libcsamfile.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcsamfile.c:1870:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-2.7/pysam/samfile_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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcalignmentfile.c:4:
pysam/libcalignmentfile.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcalignmentfile.c:2269:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23791:21: 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));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:22347:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:7474:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-2.7/pysam/samfile_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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcalignedsegment.c:4:
pysam/libcalignedsegment.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcalignedsegment.c:2719:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-2.7/pysam/samfile_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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabix.pyx to pysam/libctabix.c
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libctabix.c:4:
pysam/libctabix.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libctabix.c:2163:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:6120:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libctabixproxies.c:4:
pysam/libctabixproxies.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libctabixproxies.c:1574:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcvcf.c:4:
pysam/libcvcf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcvcf.c:2128:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.66’:
pysam/libcvcf.c:24041:16: 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_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcbcf.c:4:
pysam/libcbcf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcbcf.c:2626:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:30495:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
                 from pysam/libcbcf.c:439:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcbgzf.c:4:
pysam/libcbgzf.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcbgzf.c:1140:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcfaidx.c:4:
pysam/libcfaidx.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcfaidx.c:1576:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamtools.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-armhf-2.7/pysam/libcbcftools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘init_data’,
    inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5:
bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
         args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
                                       ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/bits/string2.h:319:0,
                 from /usr/include/string.h:630,
                 from bcftools/vcfcall.c.pysam.c:28:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:427:14: note: in a call to allocation function ‘malloc’ declared here
 extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
              ^~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam_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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcftools.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcutils.pyx to pysam/libcutils.c
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:78:0,
                 from pysam/libcutils.c:4:
pysam/libcutils.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
pysam/libcutils.c:1293:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:10574:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5493:7: 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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_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 -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
I: pybuild base:184: /usr/bin/python3.6 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/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/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/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-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/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
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.6
creating build/temp.linux-armhf-3.6/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.6/pysam/libchtslib.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libchtslib.o build/temp.linux-armhf-3.6/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libchtslib.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.6/pysam/libcsamfile.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamfile.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamfile.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23791:21: 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));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:22347:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:7474:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignmentfile.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.6m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.6/pysam/samfile_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o build/temp.linux-armhf-3.6/pysam/htslib_util.o build/temp.linux-armhf-3.6/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcalignedsegment.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-armhf-3.6/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:6120:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/tabix_util.c -o build/temp.linux-armhf-3.6/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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabix.o build/temp.linux-armhf-3.6/pysam/tabix_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabix.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.6/pysam/libctabixproxies.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libctabixproxies.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.6/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.68’:
pysam/libcvcf.c:24041:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcvcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.6/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:30495:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
                 from pysam/libcbcf.c:439:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbgzf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.6/pysam/libcfaidx.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcfaidx.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcfaidx.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.6/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.6/pysam/libcsamtools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam_utils.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_index.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamtools.o build/temp.linux-armhf-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/padding.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.6/samtools/dict.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats.c.pysam.o build/temp.linux-armhf-3.6/samtools/sample.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.6/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.6/samtools/phase.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.6/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_index.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcsamtools.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.6/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.6/pysam/libcbcftools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/csq.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bam_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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.6/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/hclust.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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcftools.o build/temp.linux-armhf-3.6/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.6/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.6/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.6/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.6/bcftools/main.c.pysam.o build/temp.linux-armhf-3.6/bcftools/em.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.6/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.6/bcftools/hclust.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcbcftools.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-armhf-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5493:7: 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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.6/pysam/pysam_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 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcutils.o build/temp.linux-armhf-3.6/pysam/pysam_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcsamtools.cpython-36m-arm-linux-gnueabihf -lcbcftools.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.6/build/pysam/libcutils.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
I: pybuild base:184: /usr/bin/python3 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.11.2.2+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/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+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-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.11.2.2+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
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.5
creating build/temp.linux-armhf-3.5/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libchtslib.c -o build/temp.linux-armhf-3.5/pysam/libchtslib.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libchtslib.o build/temp.linux-armhf-3.5/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcsamfile.c -o build/temp.linux-armhf-3.5/pysam/libcsamfile.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-3.5/pysam/samfile_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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcsamfile.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcalignmentfile.c -o build/temp.linux-armhf-3.5/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23791:21: 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));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:22347:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:7474:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-3.5/pysam/samfile_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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcalignmentfile.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcalignedsegment.c -o build/temp.linux-armhf-3.5/pysam/libcalignedsegment.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-3.5/pysam/samfile_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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcalignedsegment.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libctabix.c -o build/temp.linux-armhf-3.5/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:6120:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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-armhf-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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libctabix.o build/temp.linux-armhf-3.5/pysam/tabix_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.5/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcvcf.c -o build/temp.linux-armhf-3.5/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.68’:
pysam/libcvcf.c:24041:16: 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_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcbcf.c -o build/temp.linux-armhf-3.5/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:30495:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
                 from pysam/libcbcf.c:439:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcbgzf.c -o build/temp.linux-armhf-3.5/pysam/libcbgzf.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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.5/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcfaidx.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.5/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.5/pysam/libcsamtools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sam_utils.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcsamtools.o build/temp.linux-armhf-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam.c.pysam.o build/temp.linux-armhf-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.5/samtools/padding.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.5/samtools/dict.c.pysam.o build/temp.linux-armhf-3.5/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.5/samtools/stats.c.pysam.o build/temp.linux-armhf-3.5/samtools/sample.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.5/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.5/samtools/phase.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_index.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamtools.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.5/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.5/pysam/libcbcftools.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/bin.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/csq.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/bam_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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/regidx.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/mpileup.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/smpl_ilist.c.pysam.o -Wno-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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/hclust.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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcbcftools.o build/temp.linux-armhf-3.5/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.5/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.5/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.5/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.5/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.5/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.5/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.5/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.5/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.5/bcftools/main.c.pysam.o build/temp.linux-armhf-3.5/bcftools/em.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.5/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.5/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.5/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.5/bcftools/version.c.pysam.o build/temp.linux-armhf-3.5/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.5/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.5/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.5/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.5/bcftools/hclust.c.pysam.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcftools.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/libcutils.c -o build/temp.linux-armhf-3.5/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5493:7: 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 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -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/pysam_util.c -o build/temp.linux-armhf-3.5/pysam/pysam_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 -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcutils.o build/temp.linux-armhf-3.5/pysam/pysam_util.o -Lpysam -L/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam -lz -lhts -lchtslib.cpython-35m-arm-linux-gnueabihf -lcsamtools.cpython-35m-arm-linux-gnueabihf -lcbcftools.cpython-35m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+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 ex9_nofail.sam > ex9_nofail.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 ex6.sam > ex6.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex_spliced.sam > ex_spliced.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 ex4.sam > ex4.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 ex9_nofail.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 ex6.bam
samtools index rg_with_tab.bam
samtools index ex_spliced.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex4.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
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+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-0.11.2.2+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:184: cd /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose 
reference bases should always be the same nucleotide ... ok
testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok
check comparison functions. ... ok
testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok
see issue 26 ... ok
testHashing (AlignedSegment_test.TestAlignedSegment) ... ok
build an example read. ... ok
issue 176: retrieving length without query sequence ... ok
testPositions (AlignedSegment_test.TestAlignedSegment) ... ok
see issue 62 ... ok
testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok
check if updating fields affects other variable length data ... ok
issue 135: inplace update of sequence and quality score. ... ok
check if updating tlen works ... ok
test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok
Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok
Test infer_read_length on M|=|X|I|D|H|S cigar ops ... ok
test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok
testAsString (AlignedSegment_test.TestAsString) ... ok
testStats (AlignedSegment_test.TestCigarStats) ... ok
testCopy (AlignedSegment_test.TestCopy) ... ok
testDeepCopy (AlignedSegment_test.TestCopy) ... ok
test_cigar_enums_are_defined (AlignedSegment_test.TestEnums) ... ok
test_sam_flags_are_defined (AlignedSegment_test.TestEnums) ... ok
testAddTags (AlignedSegment_test.TestTags) ... ok
testAddTagsType (AlignedSegment_test.TestTags) ... ok
testArrayTags (AlignedSegment_test.TestTags) ... ok
testEmptyTag (AlignedSegment_test.TestTags) ... ok
testMDTagComplex (AlignedSegment_test.TestTags) ... ok
testMDTagDeletions (AlignedSegment_test.TestTags) ... ok
testMDTagInsertions (AlignedSegment_test.TestTags) ... ok
testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok
testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok
testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok
testMissingTag (AlignedSegment_test.TestTags) ... ok
testSetTag (AlignedSegment_test.TestTags) ... ok
test for tag parsing ... ok
testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARcigar (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARflag (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARmapq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARmpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARmrnm (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARpos (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARqname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARqqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARqual (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARquery (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARrname (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARseq (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testOpt (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testPairedBools (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testTags (AlignmentFile_test.BasicTestCRAMFromFetch) ... ok
testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARcigar (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARflag (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARmapq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARmpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARmrnm (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARpos (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARqname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARqqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARqual (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARquery (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARrname (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARseq (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testOpt (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testPairedBools (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testTags (AlignmentFile_test.BasicTestCRAMFromFile) ... ok
testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARcigar (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARflag (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARmapq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARmpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARmrnm (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARpos (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARqname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARqqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARqual (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARquery (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARrname (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARseq (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testOpt (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testPairedBools (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testTags (AlignmentFile_test.BasicTestCRAMFromFileNo) ... ok
testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARcigar (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARcigarstring (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARflag (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARmapq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARmpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARmrnm (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARpos (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARqname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARqqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARqual (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARquery (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARrname (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARseq (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testOpt (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testPairedBools (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testTags (AlignmentFile_test.BasicTestCRAMFromFilename) ... ok
testARQueryLength (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARcigar (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARcigarstring (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARflag (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARmapq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARmpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARmrnm (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARpos (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARqname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARqqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARqual (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARquery (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARrname (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARseq (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testOpt (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testPairedBools (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testTags (AlignmentFile_test.BasicTestSAMFromFetch) ... ok
testARQueryLength (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARcigar (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARcigarstring (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARflag (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARmapq (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARmpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARmrnm (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARpos (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARqname (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARqqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARqual (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARquery (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARrname (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARseq (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testOpt (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testPairedBools (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testTags (AlignmentFile_test.BasicTestSAMFromFile) ... ok
testARQueryLength (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARcigar (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARcigarstring (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARflag (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARmapq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARmpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARmrnm (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARpos (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARqname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARqqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARqual (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARquery (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARrname (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARseq (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testOpt (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testPairedBools (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testTags (AlignmentFile_test.BasicTestSAMFromFileNo) ... ok
testARQueryLength (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARcigar (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARcigarstring (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARflag (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARmapq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARmpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARmrnm (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARpos (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARqname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARqqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARqual (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARquery (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARrname (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARseq (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testOpt (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testPairedBools (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testTags (AlignmentFile_test.BasicTestSAMFromFilename) ... ok
testARQueryLength (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARcigar (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARcigarstring (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARflag (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARmapq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARmpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARmrnm (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARpos (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARqname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARqqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARqual (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARquery (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARrname (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testARseq (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testOpt (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testPairedBools (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testRaises (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testTags (AlignmentFile_test.BasicTestSAMFromStringIO) ... ok
testIndex (AlignmentFile_test.TestAlignmentFileIndex) ... ok
testCount (AlignmentFile_test.TestAlignmentFileUtilityFunctions) ... ok
test if total number of mapped/unmapped reads is correct. ... ok
test mate access. ... ok
test BAM autodetection. ... ok
test CRAM autodetection. ... ok
test SAM autodetection. ... ok
testReadTags (AlignmentFile_test.TestBTagBam) ... ok
testReadWriteTags (AlignmentFile_test.TestBTagBam) ... ok
testReadTags (AlignmentFile_test.TestBTagSam) ... ok
testReadWriteTags (AlignmentFile_test.TestBTagSam) ... ok
testClipping (AlignmentFile_test.TestClipping) ... ok
testManager (AlignmentFile_test.TestContextManager) ... ok
test_count_coverage (AlignmentFile_test.TestCountCoverage) ... ok
test_count_coverage_nofilter (AlignmentFile_test.TestCountCoverage) ... ok
test_count_coverage_quality_filter (AlignmentFile_test.TestCountCoverage) ... ok
test_count_coverage_read_all (AlignmentFile_test.TestCountCoverage) ... ok
test_count_coverage_read_callback (AlignmentFile_test.TestCountCoverage) ... ok
testBAMWholeFile (AlignmentFile_test.TestDeNovoConstruction) ... ok
check if individual reads are binary equal. ... ok
testBAMWholeFile (AlignmentFile_test.TestDeNovoConstructionUserTags) ... ok
check if individual reads are binary equal. ... ok
testDoubleFetch (AlignmentFile_test.TestDoubleFetchBAM) ... ok
testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchBAM) ... ok
testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchBAM) ... ok
testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAM) ... ok
testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAM) ... ok
testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAM) ... ok
testDoubleFetch (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok
testDoubleFetchUntilEOF (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok
testDoubleFetchWithRegion (AlignmentFile_test.TestDoubleFetchCRAMWithReference) ... ok
testEmptyHeader (AlignmentFile_test.TestEmptyHeader) ... ok
testBackwardsOrderNewFormat (AlignmentFile_test.TestExceptions) ... ok
testBackwardsOrderOldFormat (AlignmentFile_test.TestExceptions) ... ok
testBadContig (AlignmentFile_test.TestExceptions) ... ok
testMeaninglessCrap (AlignmentFile_test.TestExceptions) ... ok
testMissingFile (AlignmentFile_test.TestExceptions) ... ok
testOutOfRangNewFormat (AlignmentFile_test.TestExceptions) ... ok
testOutOfRangeLargeNewFormat (AlignmentFile_test.TestExceptions) ... ok
testOutOfRangeLargeOldFormat (AlignmentFile_test.TestExceptions) ... ok
testOutOfRangeNegativeNewFormat (AlignmentFile_test.TestExceptions) ... ok
testOutOfRangeNegativeOldFormat (AlignmentFile_test.TestExceptions) ... ok
see issue 44 ... ok
testExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... Warning: The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/pysam_data/ex1.bam.bai
ok
testExplicitIndexCRAM (AlignmentFile_test.TestExplicitIndex) ... ok
testRemoteExplicitIndexBAM (AlignmentFile_test.TestExplicitIndex) ... ok
test_all (AlignmentFile_test.TestFindIntrons) ... ok
test_first (AlignmentFile_test.TestFindIntrons) ... ok
test_total (AlignmentFile_test.TestFindIntrons) ... ok
a float tag before another exposed a parsing bug in bam_aux_get. ... ok
testRead (AlignmentFile_test.TestHeader1000Genomes) ... ok
testHeaders (AlignmentFile_test.TestHeaderBAM) ... ok
testNameMapping (AlignmentFile_test.TestHeaderBAM) ... ok
testHeaders (AlignmentFile_test.TestHeaderCRAM) ... ok
testNameMapping (AlignmentFile_test.TestHeaderCRAM) ... ok
testHeaders (AlignmentFile_test.TestHeaderSAM) ... ok
testNameMapping (AlignmentFile_test.TestHeaderSAM) ... ok
testHeader (AlignmentFile_test.TestHeaderWithProgramOptions) ... ok
test_BAM (AlignmentFile_test.TestHeaderWriteRead) ... ok
test_CRAM (AlignmentFile_test.TestHeaderWriteRead) ... ok
test_SAM (AlignmentFile_test.TestHeaderWriteRead) ... ok
testBAM2BAM (AlignmentFile_test.TestIO) ... ok
testBAM2CRAM (AlignmentFile_test.TestIO) ... ok
testBAM2SAM (AlignmentFile_test.TestIO) ... ok
see issue 116 ... ok
see issue 116 ... ok
see issue 117 ... ok
testCRAM2BAM (AlignmentFile_test.TestIO) ... ok
testCRAM2CRAM (AlignmentFile_test.TestIO) ... ok
testCRAM2SAM (AlignmentFile_test.TestIO) ... ok
test that access to a closed samfile raises ValueError. ... ok
testEmptyBAM (AlignmentFile_test.TestIO) ... ok
testEmptyWithHeaderBAM (AlignmentFile_test.TestIO) ... ok
testFetchFromClosedFile (AlignmentFile_test.TestIO) ... ok
testFetchFromClosedFileObject (AlignmentFile_test.TestIO) ... ok
test IteratorRowHead ... ok
testOpenFromFilename (AlignmentFile_test.TestIO) ... ok
see issue 104. ... ok
see issue 104. ... ok
read from bam file without index. ... ok
testSAM2BAM (AlignmentFile_test.TestIO) ... ok
testSAM2CRAM (AlignmentFile_test.TestIO) ... ok
testSAM2SAM (AlignmentFile_test.TestIO) ... ok
testSAM2SAMWithoutHeader (AlignmentFile_test.TestIO) ... ok
read from uncompressed BAM file, see issue #43 ... ok
test_fail_read_sam_without_header (AlignmentFile_test.TestIO) ... ok
test reading from a file that is not bam/sam formatted ... ok
test_fetch_by_tid (AlignmentFile_test.TestIO) ... ok
test_pass_read_sam_with_header_without_header_check (AlignmentFile_test.TestIO) ... ok
test_pass_read_sam_without_header_with_refs (AlignmentFile_test.TestIO) ... ok
see issue 131 ... ok
testStart (AlignmentFile_test.TestIteratorColumn2) ... ok
test if PileupRead can be printed. ... ok
see issue 107. ... ok
test the inverse, is point-wise pileup accurate. ... ok
check random access per contig ... ok
check random access per contig ... ok
check random access per range ... ok
check random access per range ... ok
compare results from iterator with those from samtools. ... ok
check random access per contig ... ok
check random access per range ... ok
check random access per contig ... ok
check random access per range ... ok
check random access per contig ... ok
check random access per range ... ok
when creating a read with a large entry in the tag field ... ok
testBAM (AlignmentFile_test.TestLargeOptValues) ... ok
testSAM (AlignmentFile_test.TestLargeOptValues) ... ok
testFail1 (AlignmentFile_test.TestLogging) ... ok
testNoFail1 (AlignmentFile_test.TestLogging) ... ok
testNoFail2 (AlignmentFile_test.TestLogging) ... ok
testMapped (AlignmentFile_test.TestMappedUnmapped) ... ok
testAllStepper (AlignmentFile_test.TestPileup) ... ok
testSamtoolsStepper (AlignmentFile_test.TestPileup) ... ok
test if exception is raised if pileup col is accessed after ... ok
testPileupColumn (AlignmentFile_test.TestPileupObjects) ... ok
testPileupRead (AlignmentFile_test.TestPileupObjects) ... ok
testPileup (AlignmentFile_test.TestPileupQueryPosition) ... ok
testFTPFetch (AlignmentFile_test.TestRemoteFileFTP) ... ok
testFTPView (AlignmentFile_test.TestRemoteFileFTP) ... ok
testFetch (AlignmentFile_test.TestRemoteFileHTTP) ... ok
testFetchAll (AlignmentFile_test.TestRemoteFileHTTP) ... ok
testView (AlignmentFile_test.TestRemoteFileHTTP) ... ok
testIndex (AlignmentFile_test.TestSamtoolsProxy) ... ok
testSort (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file'
ok
testView (AlignmentFile_test.TestSamtoolsProxy) ... [E::hts_open_format] fail to open file 'missing_file'
ok
test_empty_read_gives_value_error (AlignmentFile_test.TestSanityCheckingBAM) ... ok
testArrayTags (AlignmentFile_test.TestTagParsing) ... ok
testCigar (AlignmentFile_test.TestTagParsing) ... ok
testCigarString (AlignmentFile_test.TestTagParsing) ... ok
see issue 115 ... ok
testNegativeIntegers (AlignmentFile_test.TestTagParsing) ... ok
testNegativeIntegers2 (AlignmentFile_test.TestTagParsing) ... ok
testTruncatedBam2 (AlignmentFile_test.TestTruncatedBAM) ... /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/AlignmentFile_test.py:1863: UserWarning: no BGZF EOF marker; file may be truncated
  ignore_truncation=True)
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes
ok
testBAM (AlignmentFile_test.TestUnmappedReads) ... ok
testVerbosity (AlignmentFile_test.TestVerbosity) ... ok
testOpenBamAsSam (AlignmentFile_test.TestWrongFormat) ... ok
testOpenFastaAsBam (AlignmentFile_test.TestWrongFormat) ... ok
testOpenFastaAsSam (AlignmentFile_test.TestWrongFormat) ... ok
testOpenSamAsBam (AlignmentFile_test.TestWrongFormat) ... ok
test_samtools_processing (StreamFiledescriptors_test.StreamTest) ... SKIP: test contains bug
test_text_processing (StreamFiledescriptors_test.StreamTest) ... SKIP: no context manager in py2
testBase (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok
testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok
testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok
testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithContigs) ... ok
testBase (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok
testConstructionFromCopy (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok
testConstructionWithLines (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok
testConstructionWithRecords (VariantFile_test.TestConstructionVCFGZWithoutContigs) ... ok
testBase (VariantFile_test.TestConstructionVCFWithContigs) ... ok
testConstructionFromCopy (VariantFile_test.TestConstructionVCFWithContigs) ... ok
testConstructionWithLines (VariantFile_test.TestConstructionVCFWithContigs) ... ok
testConstructionWithRecords (VariantFile_test.TestConstructionVCFWithContigs) ... ok
testIterator (VariantFile_test.TestHeader) ... ok
testStr (VariantFile_test.TestHeader) ... ok
testOpen (VariantFile_test.TestIndexFilename) ... ok
testVCF (VariantFile_test.TestMissingGenotypes) ... ok
testVCFGZ (VariantFile_test.TestMissingGenotypes) ... ok
testDetectBCF (VariantFile_test.TestOpening) ... ok
testDetectVCF (VariantFile_test.TestOpening) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testDetectVCFGZ (VariantFile_test.TestOpening) ... ok
testEmptyFileVCF (VariantFile_test.TestOpening) ... ok
testEmptyFileVCFGZOnlyHeader (VariantFile_test.TestOpening) ... ok
testEmptyFileVCFGZWithIndex (VariantFile_test.TestOpening) ... ok
testEmptyFileVCFGZWithoutIndex (VariantFile_test.TestOpening) ... ok
testEmptyFileVCFOnlyHeader (VariantFile_test.TestOpening) ... ok
testMissingFile (VariantFile_test.TestOpening) ... ok
testMissingFileVCFGZ (VariantFile_test.TestOpening) ... ok
testAlleles (VariantFile_test.TestParsing) ... ok
testAlt (VariantFile_test.TestParsing) ... ok
testChrom (VariantFile_test.TestParsing) ... ok
testFilter (VariantFile_test.TestParsing) ... ok
testFormat (VariantFile_test.TestParsing) ... ok
testId (VariantFile_test.TestParsing) ... ok
testInfo (VariantFile_test.TestParsing) ... ok
testPos (VariantFile_test.TestParsing) ... ok
testQual (VariantFile_test.TestParsing) ... ok
testRef (VariantFile_test.TestParsing) ... ok
testSampleAlleleIndices (VariantFile_test.TestParsing) ... ok
testSampleAlleles (VariantFile_test.TestParsing) ... ok
testSampleFormats (VariantFile_test.TestParsing) ... ok
testStart (VariantFile_test.TestParsing) ... ok
testStop (VariantFile_test.TestParsing) ... ok
testBase (VariantFile_test.TestSettingRecordValues) ... ok
testGenotype (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
ERROR
testSetQual (VariantFile_test.TestSettingRecordValues) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testSubsetting (VariantFile_test.TestSubsetting) ... ok
In file included from /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/_compile_test.c:440:0:
/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^~~
In file included from /usr/include/python2.7/Python.h:78:0,
                 from /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/_compile_test.c:4:
/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/_compile_test.c: In function ‘newarrayobject’:
/usr/include/python2.7/pymem.h:97:30: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context]
  ( (type *) PyMem_MALLOC((n) * sizeof(type)) ) )
                              ^
/usr/include/python2.7/pymem.h:75:15: note: in definition of macro ‘PyMem_MALLOC’
     : malloc((n) ? (n) : 1))
               ^
/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/_compile_test.c:2027:28: note: in expansion of macro ‘PyMem_NEW’
         op->data.ob_item = PyMem_NEW(char, nbytes);
                            ^~~~~~~~~
testCount (compile_test.BAMTest) ... ok
testCount (compile_test.GTFTest) ... ok
testFetch (faidx_test.TestFastaFile) ... ok
testFetchErrors (faidx_test.TestFastaFile) ... ok
testLength (faidx_test.TestFastaFile) ... ok
test out of range access. ... ok
testSequenceLengths (faidx_test.TestFastaFile) ... ok
testGarbageIndex (faidx_test.TestFastaFilePathIndex) ... ok
testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndex) ... ok
testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndex) ... ok
testOpenWithoutIndex (faidx_test.TestFastaFilePathIndex) ... ok
testGarbageIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok
testOpenWithOtherIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok
testOpenWithStandardIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok
testOpenWithoutIndex (faidx_test.TestFastaFilePathIndexCompressed) ... ok
testCounts (faidx_test.TestFastqFileFastq) ... ok
testManager (faidx_test.TestFastqFileFastq) ... ok
testMissingFile (faidx_test.TestFastqFileFastq) ... ok
testSequence (faidx_test.TestFastqFileFastq) ... ok
testCounts (faidx_test.TestFastxFileFasta) ... ok
testManager (faidx_test.TestFastxFileFasta) ... ok
testMissingFile (faidx_test.TestFastxFileFasta) ... ok
testSequence (faidx_test.TestFastxFileFasta) ... ok
testCounts (faidx_test.TestFastxFileFastq) ... ok
testManager (faidx_test.TestFastxFileFastq) ... ok
testMissingFile (faidx_test.TestFastxFileFastq) ... ok
testSequence (faidx_test.TestFastxFileFastq) ... ok
testCounts (faidx_test.TestFastxFileFastqStream) ... ok
testManager (faidx_test.TestFastxFileFastqStream) ... ok
testMissingFile (faidx_test.TestFastxFileFastqStream) ... ok
testSequence (faidx_test.TestFastxFileFastqStream) ... ok
testIteration (faidx_test.TestFastxFileWithEmptySequence) ... ok
testFTPView (faidx_test.TestRemoteFileFTP) ... ok
test_sequence_lengths_are_available (faidx_test.TestRemoteFileFTP) ... ok
testStatements (samtools_test.BcftoolsTest) ... [W::bcf_hdr_check_sanity] GL should be declared as Number=G
ok
testUsage (samtools_test.BcftoolsTest) ... SKIP: skipping usage tests, stdin is not a tty
testEmptyIndex (samtools_test.EmptyIndexTest) ... ok
testStatements (samtools_test.PysamTest) ... ok
testUsage (samtools_test.PysamTest) ... SKIP: skipping usage tests, stdin is not a tty
testStatements (samtools_test.SamtoolsTest) ... ok
testUsage (samtools_test.SamtoolsTest) ... SKIP: skipping usage tests, stdin is not a tty
testDoubleCalling (samtools_test.StdoutTest) ... ok
testSaveStdout (samtools_test.StdoutTest) ... ok
testWithRedirectedStdout (samtools_test.StdoutTest) ... ok
testWithoutRedirectedStdout (samtools_test.StdoutTest) ... ok
testReturnValueData (samtools_test.TestReturnType) ... ok
testReturnValueString (samtools_test.TestReturnType) ... ok
testBED (tabix_test.TestBackwardsCompatibility) ... ok
testBED0v23 (tabix_test.TestBackwardsCompatibility) ... ok
testBED0v26 (tabix_test.TestBackwardsCompatibility) ... ok
testEmpty (tabix_test.TestBackwardsCompatibility) ... ok
testVCF (tabix_test.TestBackwardsCompatibility) ... ok
testVCF0v23 (tabix_test.TestBackwardsCompatibility) ... ok
testVCF0v26 (tabix_test.TestBackwardsCompatibility) ... ok
testRead (tabix_test.TestBed) ... ok
testWrite (tabix_test.TestBed) ... ok
see also issue 106 ... ok
test indexing via preset. ... ok
test indexing via preset. ... ok
see also issue 106 ... ok
test indexing via preset. ... ok
test indexing via preset. ... ok
see also issue 106 ... ok
test indexing via preset. ... ok
test indexing via preset. ... ok
see also issue 106 ... ok
test indexing via preset. ... ok
test indexing via preset. ... ok
testManager (tabix_test.TestContextManager) ... ok
testAll (tabix_test.TestGZFile) ... ok
testFetchAll (tabix_test.TestIndexArgument) ... ok
test indexing via preset. ... ok
testGTFTooFewFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok
testGTFTooManyFields (tabix_test.TestIterationMalformattedGTFFiles) ... ok
testAll (tabix_test.TestIterationWithComments) ... ok
testGetContigs (tabix_test.TestIterationWithComments) ... ok
testHeader (tabix_test.TestIterationWithComments) ... ok
testInvalidIntervals (tabix_test.TestIterationWithComments) ... ok
testPerContig (tabix_test.TestIterationWithComments) ... ok
testPerContig2 (tabix_test.TestIterationWithComments) ... ok
testPerContigFromStart (tabix_test.TestIterationWithComments) ... ok
testPerContigToEnd (tabix_test.TestIterationWithComments) ... ok
testPerInterval (tabix_test.TestIterationWithComments) ... ok
test if access with various region strings ... ok
test repeated opening of the same file. ... ok
testAll (tabix_test.TestIterationWithoutComments) ... ok
testGetContigs (tabix_test.TestIterationWithoutComments) ... ok
testHeader (tabix_test.TestIterationWithoutComments) ... ok
testInvalidIntervals (tabix_test.TestIterationWithoutComments) ... ok
testPerContig (tabix_test.TestIterationWithoutComments) ... ok
testPerContig2 (tabix_test.TestIterationWithoutComments) ... ok
testPerContigFromStart (tabix_test.TestIterationWithoutComments) ... ok
testPerContigToEnd (tabix_test.TestIterationWithoutComments) ... ok
testPerInterval (tabix_test.TestIterationWithoutComments) ... ok
test if access with various region strings ... ok
test repeated opening of the same file. ... ok
test for error when iterating from closed file. ... ok
test for error when iterating from file that has been closed ... ok
testIteration (tabix_test.TestIterators) ... ok
test for error when iterating from closed file. ... ok
test for error when iterating from file that has been closed ... ok
testIteration (tabix_test.TestIteratorsFileCompressed) ... ok
test for error when iterating from closed file. ... ok
test for error when iterating from file that has been closed ... ok
testIteration (tabix_test.TestIteratorsFileUncompressed) ... ok
test for error when iterating from closed file. ... ok
test for error when iterating from file that has been closed ... ok
testIteration (tabix_test.TestIteratorsGenericCompressed) ... ok
testDisjointIterators (tabix_test.TestMultipleIterators) ... ok
testDoubleFetch (tabix_test.TestMultipleIterators) ... ok
testJoinedIterators (tabix_test.TestMultipleIterators) ... ok
testScope (tabix_test.TestMultipleIterators) ... ok
testFetchAll (tabix_test.TestRemoteFileHTTP) ... ok
testHeader (tabix_test.TestRemoteFileHTTP) ... ok
testRead (tabix_test.TestVCFFromTabix) ... ok
testWrite (tabix_test.TestVCFFromTabix) ... ok
testConnecting (tabix_test.TestVCFFromVCF) ... ok
testParsing (tabix_test.TestVCFFromVCF) ... ok
testConnecting (tabix_test.TestVCFFromVariantFile) ... ok
testParsing (tabix_test.TestVCFFromVariantFile) ... [W::vcf_parse] contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_10) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_10) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_11) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_11) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_12) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_12) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_13) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_13) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_15) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_15) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_16) ... [W::bcf_hdr_check_sanity] PL should be declared as Number=G
ok
testParsing (tabix_test.TestVCFFromVariantFile_16) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_18) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_18) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_2) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_2) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_20) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_20) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_21) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_21) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_22) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_22) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_23) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_23) ... [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_24) ... [W::bcf_hdr_parse] Couldn't parse header line: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
ok
testParsing (tabix_test.TestVCFFromVariantFile_24) ... ok
testConnecting (tabix_test.TestVCFFromVariantFile_3) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_3) ... [W::vcf_parse] contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_4) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_4) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_5) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_5) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_6) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_6) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_7) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_7) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_8) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_8) ... [W::vcf_parse] contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
ok
testConnecting (tabix_test.TestVCFFromVariantFile_9) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_9) ... [W::vcf_parse] contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
ok
testConnecting (tabix_test.TestVCFFromVariantFile_issue85) ... [E::bcf_hdr_parse] Could not parse the header, sample line not found
ok
testParsing (tabix_test.TestVCFFromVariantFile_issue85) ... ok
testConnecting (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok
testParsing (tabix_test.TestVCFFromVariantFile_vcf_v42) ... ok
testRead (tabix_test.VCFFromTabixTest_10) ... ok
testWrite (tabix_test.VCFFromTabixTest_10) ... ok
testRead (tabix_test.VCFFromTabixTest_11) ... ok
testWrite (tabix_test.VCFFromTabixTest_11) ... ok
testRead (tabix_test.VCFFromTabixTest_12) ... ok
testWrite (tabix_test.VCFFromTabixTest_12) ... ok
testRead (tabix_test.VCFFromTabixTest_13) ... ok
testWrite (tabix_test.VCFFromTabixTest_13) ... ok
testRead (tabix_test.VCFFromTabixTest_15) ... ok
testWrite (tabix_test.VCFFromTabixTest_15) ... ok
testRead (tabix_test.VCFFromTabixTest_16) ... ok
testWrite (tabix_test.VCFFromTabixTest_16) ... ok
testRead (tabix_test.VCFFromTabixTest_18) ... ok
testWrite (tabix_test.VCFFromTabixTest_18) ... ok
testRead (tabix_test.VCFFromTabixTest_2) ... ok
testWrite (tabix_test.VCFFromTabixTest_2) ... ok
testRead (tabix_test.VCFFromTabixTest_20) ... ok
testWrite (tabix_test.VCFFromTabixTest_20) ... ok
testRead (tabix_test.VCFFromTabixTest_21) ... ok
testWrite (tabix_test.VCFFromTabixTest_21) ... ok
testRead (tabix_test.VCFFromTabixTest_22) ... ok
testWrite (tabix_test.VCFFromTabixTest_22) ... ok
testRead (tabix_test.VCFFromTabixTest_23) ... ok
testWrite (tabix_test.VCFFromTabixTest_23) ... ok
testRead (tabix_test.VCFFromTabixTest_24) ... ok
testWrite (tabix_test.VCFFromTabixTest_24) ... ok
testRead (tabix_test.VCFFromTabixTest_3) ... ok
testWrite (tabix_test.VCFFromTabixTest_3) ... ok
testRead (tabix_test.VCFFromTabixTest_4) ... ok
testWrite (tabix_test.VCFFromTabixTest_4) ... ok
testRead (tabix_test.VCFFromTabixTest_5) ... ok
testWrite (tabix_test.VCFFromTabixTest_5) ... ok
testRead (tabix_test.VCFFromTabixTest_6) ... ok
testWrite (tabix_test.VCFFromTabixTest_6) ... ok
testRead (tabix_test.VCFFromTabixTest_7) ... ok
testWrite (tabix_test.VCFFromTabixTest_7) ... ok
testRead (tabix_test.VCFFromTabixTest_8) ... ok
testWrite (tabix_test.VCFFromTabixTest_8) ... ok
testRead (tabix_test.VCFFromTabixTest_9) ... ok
testWrite (tabix_test.VCFFromTabixTest_9) ... ok
testRead (tabix_test.VCFFromTabixTest_issue85) ... ok
testWrite (tabix_test.VCFFromTabixTest_issue85) ... ok
testRead (tabix_test.VCFFromTabixTest_vcf_v42) ... ok
testWrite (tabix_test.VCFFromTabixTest_vcf_v42) ... ok
testConnecting (tabix_test.VCFFromVCFTest_10) ... ok
testParsing (tabix_test.VCFFromVCFTest_10) ... ok
testConnecting (tabix_test.VCFFromVCFTest_11) ... ok
testParsing (tabix_test.VCFFromVCFTest_11) ... ok
testConnecting (tabix_test.VCFFromVCFTest_12) ... ok
testParsing (tabix_test.VCFFromVCFTest_12) ... ok
testConnecting (tabix_test.VCFFromVCFTest_13) ... ok
testParsing (tabix_test.VCFFromVCFTest_13) ... ok
testConnecting (tabix_test.VCFFromVCFTest_15) ... ok
testParsing (tabix_test.VCFFromVCFTest_15) ... ok
testConnecting (tabix_test.VCFFromVCFTest_16) ... ok
testParsing (tabix_test.VCFFromVCFTest_16) ... ok
testConnecting (tabix_test.VCFFromVCFTest_18) ... ok
testParsing (tabix_test.VCFFromVCFTest_18) ... ok
testConnecting (tabix_test.VCFFromVCFTest_2) ... ok
testParsing (tabix_test.VCFFromVCFTest_2) ... ok
testConnecting (tabix_test.VCFFromVCFTest_20) ... ok
testParsing (tabix_test.VCFFromVCFTest_20) ... ok
testConnecting (tabix_test.VCFFromVCFTest_21) ... ok
testParsing (tabix_test.VCFFromVCFTest_21) ... ok
testConnecting (tabix_test.VCFFromVCFTest_22) ... ok
testParsing (tabix_test.VCFFromVCFTest_22) ... ok
testConnecting (tabix_test.VCFFromVCFTest_23) ... ok
testParsing (tabix_test.VCFFromVCFTest_23) ... ok
testConnecting (tabix_test.VCFFromVCFTest_24) ... ok
testParsing (tabix_test.VCFFromVCFTest_24) ... ok
testConnecting (tabix_test.VCFFromVCFTest_3) ... ok
testParsing (tabix_test.VCFFromVCFTest_3) ... ok
testConnecting (tabix_test.VCFFromVCFTest_4) ... ok
testParsing (tabix_test.VCFFromVCFTest_4) ... ok
testConnecting (tabix_test.VCFFromVCFTest_5) ... ok
testParsing (tabix_test.VCFFromVCFTest_5) ... ok
testConnecting (tabix_test.VCFFromVCFTest_6) ... ok
testParsing (tabix_test.VCFFromVCFTest_6) ... ok
testConnecting (tabix_test.VCFFromVCFTest_7) ... ok
testParsing (tabix_test.VCFFromVCFTest_7) ... ok
testConnecting (tabix_test.VCFFromVCFTest_8) ... ok
testParsing (tabix_test.VCFFromVCFTest_8) ... ok
testConnecting (tabix_test.VCFFromVCFTest_9) ... ok
testParsing (tabix_test.VCFFromVCFTest_9) ... ok
testConnecting (tabix_test.VCFFromVCFTest_issue85) ... ok
testParsing (tabix_test.VCFFromVCFTest_issue85) ... ok
testConnecting (tabix_test.VCFFromVCFTest_vcf_v42) ... ok
testParsing (tabix_test.VCFFromVCFTest_vcf_v42) ... ok
testCopy (tabixproxies_test.TestGFF3) ... ok
test iteration from compressed file. ... ok
test iteration from uncompressed file. ... ok
testRead (tabixproxies_test.TestGFF3) ... ok
testSetting (tabixproxies_test.TestGFF3) ... ok
testUnset (tabixproxies_test.TestGFF3) ... ok
testWrite (tabixproxies_test.TestGFF3) ... ok
test_added_attribute_is_output (tabixproxies_test.TestGFF3) ... ok
test_setting_end_is_one_based (tabixproxies_test.TestGFF3) ... ok
test_setting_feature_to_none_produces_dot (tabixproxies_test.TestGFF3) ... ok
test_setting_frame_to_none_produces_dot (tabixproxies_test.TestGFF3) ... ok
test_setting_score_to_none_produces_dot (tabixproxies_test.TestGFF3) ... ok
test_setting_source_to_none_produces_dot (tabixproxies_test.TestGFF3) ... ok
test_setting_start_is_one_based (tabixproxies_test.TestGFF3) ... ok
test_setting_strand_to_none_produces_dot (tabixproxies_test.TestGFF3) ... ok
testCopy (tabixproxies_test.TestGTF) ... ok
test iteration from compressed file. ... ok
test iteration from uncompressed file. ... ok
testRead (tabixproxies_test.TestGTF) ... ok
testSetting (tabixproxies_test.TestGTF) ... ok
testUnset (tabixproxies_test.TestGTF) ... ok
testWrite (tabixproxies_test.TestGTF) ... ok
test_added_attribute_is_output (tabixproxies_test.TestGTF) ... ok
test_setting_end_is_one_based (tabixproxies_test.TestGTF) ... ok
test_setting_feature_to_none_produces_dot (tabixproxies_test.TestGTF) ... ok
test_setting_frame_to_none_produces_dot (tabixproxies_test.TestGTF) ... ok
test_setting_score_to_none_produces_dot (tabixproxies_test.TestGTF) ... ok
test_setting_source_to_none_produces_dot (tabixproxies_test.TestGTF) ... ok
test_setting_start_is_one_based (tabixproxies_test.TestGTF) ... ok
test_setting_strand_to_none_produces_dot (tabixproxies_test.TestGTF) ... ok
testCopy (tabixproxies_test.TestParser) ... ok
test iteration from compressed file. ... ok
test iteration from uncompressed file. ... ok
testRead (tabixproxies_test.TestParser) ... ok
testUnset (tabixproxies_test.TestParser) ... ok
testWrite (tabixproxies_test.TestParser) ... ok
test_samtools_python.test_idxstats_parse_split_lines ... ok
test_samtools_python.test_bedcov_split_lines ... ok
test_samtools_python.test_idxstats_parse ... ok
test_samtools_python.test_bedcov ... ok

======================================================================
ERROR: testGenotype (VariantFile_test.TestSettingRecordValues)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<BUILDDIR>>/python-pysam-0.11.2.2+ds/tests/VariantFile_test.py", line 492, in testGenotype
    sample["GT"] = sample["GT"]
  File "pysam/libcbcf.pyx", line 3413, in pysam.libcbcf.VariantRecordSample.__setitem__ (pysam/libcbcf.c:51522)
  File "pysam/libcbcf.pyx", line 854, in pysam.libcbcf.bcf_format_set_value (pysam/libcbcf.c:12977)
  File "pysam/libcbcf.pyx", line 587, in pysam.libcbcf.bcf_check_values (pysam/libcbcf.c:9846)
TypeError: invalid value for Integer format

----------------------------------------------------------------------
Ran 760 tests in 221.512s

FAILED (SKIP=5, errors=1)
(0, 0)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-pysam-0.11.2.2+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose 
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
debian/rules:39: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.11.2.2+ds'
debian/rules:33: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-10-03T03:49:13Z

Finished
--------


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

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

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

Build Architecture: armhf
Build-Space: 164376
Build-Time: 1947
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 299
Job: python-pysam_0.11.2.2+ds-3
Machine Architecture: armhf
Package: python-pysam
Package-Time: 2268
Source-Version: 0.11.2.2+ds-3
Space: 164376
Status: attempted
Version: 0.11.2.2+ds-3
--------------------------------------------------------------------------------
Finished at 2017-10-03T03:49:13Z
Build needed 00:37:48, 164376k disk space