https://launchpad.net/ubuntu/+archive/test-rebuild-20180408/+build/14618406
RUN: /usr/share/launchpad-buildd/slavebin/slave-prep 
Forking launchpad-buildd slave process...
Kernel version: Linux bos02-arm64-014 4.4.0-121-generic #145-Ubuntu SMP Fri Apr 13 13:47:48 UTC 2018 aarch64
Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2.
Syncing the system clock with the buildd NTP service...
27 Apr 09:07:56 ntpdate[1813]: adjust time server 10.211.37.1 offset 0.338905 sec
RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406 /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc
Creating target for build PACKAGEBUILD-14618406
RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406
Starting target for build PACKAGEBUILD-14618406
RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse'
Overriding sources.list in build-PACKAGEBUILD-14618406
RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406
Updating target for build PACKAGEBUILD-14618406
Get:1 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB]
Get:2 http://ftpmaster.internal/ubuntu bionic-security InRelease [65.4 kB]
Get:3 http://ftpmaster.internal/ubuntu bionic-updates InRelease [65.4 kB]
Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [968 kB]
Get:5 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB]
Get:6 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8269 kB]
Get:7 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB]
Get:8 http://ftpmaster.internal/ubuntu bionic/multiverse armhf Packages [129 kB]
Fetched 15.2 MB in 6s (2413 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14618406 armhf bionic -c chroot:build-PACKAGEBUILD-14618406 --arch=armhf --dist=bionic --nolog python-pysam_0.14+ds-2.dsc
Initiating build PACKAGEBUILD-14618406 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 4.4.0-121-generic #145-Ubuntu SMP Fri Apr 13 13:47:48 UTC 2018 armv7l
sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-014.buildd

+==============================================================================+
| python-pysam 0.14+ds-2 (armhf)                             27 Apr 2018 09:08 |
+==============================================================================+

Package: python-pysam
Version: 0.14+ds-2
Source Version: 0.14+ds-2
Distribution: bionic
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/python-pysam-3XH4be/python-pysam-0.14+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-3XH4be' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14618406/chroot-autobuild' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

python-pysam_0.14+ds-2.dsc exists in .; copying to chroot

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


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

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-kepVKK/apt_archive/sbuild-build-depends-core-dummy.deb'.
Ign:1 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ Release [2119 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ Sources [214 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ Packages [527 B]
Fetched 2860 B in 0s (132 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-kepVKK/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12378 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) ...
Merged Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.7), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.7), bcftools (>= 1.7), python-pytest, python3-pytest
Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.7), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.7), bcftools (>= 1.7), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
Ign:1 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ Release [2119 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ Sources [315 B]
Get:5 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ Packages [623 B]
Fetched 3057 B in 0s (143 kB/s)
Reading package lists...
Reading package lists...

+------------------------------------------------------------------------------+
| Install python-pysam build dependencies (apt-based resolver)                 |
+------------------------------------------------------------------------------+

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60
  libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0
  libldap-2.4-2 libldap-common liblzma-dev 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
  libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib
  libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
  libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support
  po-debconf python python-all python-all-dev python-attr python-dev
  python-funcsigs python-minimal python-pkg-resources python-pluggy python-py
  python-pytest python-setuptools python-six python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-attr
  python3-dev python3-distutils python3-lib2to3 python3-minimal
  python3-pkg-resources python3-pluggy python3-py python3-pytest
  python3-setuptools python3-six 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 dwz gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
  krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
  python-attr-doc python-funcsigs-doc subversion python-pytest-xdist
  python-mock python-setuptools-doc python2.7-doc binfmt-support python3-doc
  python3-tk python3-venv python3.6-venv python3.6-doc
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev
  libmail-sendmail-perl cwltool
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
  libasn1-8-heimdal libbsd0 libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu60
  libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0
  libldap-2.4-2 libldap-common liblzma-dev 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
  libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib
  libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
  libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support
  po-debconf python python-all python-all-dev python-attr python-dev
  python-funcsigs python-minimal python-pkg-resources python-pluggy python-py
  python-pytest python-setuptools python-six python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-attr
  python3-dev python3-distutils python3-lib2to3 python3-minimal
  python3-pkg-resources python3-pluggy python3-py python3-pytest
  python3-setuptools python3-six python3.6 python3.6-dev python3.6-minimal
  samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 114 newly installed, 0 to remove and 0 not upgraded.
Need to get 65.1 MB of archives.
After this operation, 178 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-I9Gj_C/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [952 B]
Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6-minimal armhf 3.6.5-3 [524 kB]
Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf libexpat1 armhf 2.2.5-3 [59.7 kB]
Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf python3.6-minimal armhf 3.6.5-3 [1216 kB]
Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf python3-minimal armhf 3.6.5-3 [23.8 kB]
Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf mime-support all 3.60ubuntu1 [30.1 kB]
Get:7 http://ftpmaster.internal/ubuntu bionic/main armhf libmpdec2 armhf 2.4.2-1ubuntu1 [66.4 kB]
Get:8 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6-stdlib armhf 3.6.5-3 [1595 kB]
Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf python3.6 armhf 3.6.5-3 [186 kB]
Get:10 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3-stdlib armhf 3.6.5-3 [7276 B]
Get:11 http://ftpmaster.internal/ubuntu bionic/main armhf python3 armhf 3.6.5-3 [10.2 kB]
Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libbsd0 armhf 0.8.7-1 [40.4 kB]
Get:13 http://ftpmaster.internal/ubuntu bionic/main armhf bsdmainutils armhf 11.1.2ubuntu1 [177 kB]
Get:14 http://ftpmaster.internal/ubuntu bionic/main armhf groff-base armhf 1.22.3-10 [1013 kB]
Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB]
Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf man-db armhf 2.8.3-2 [993 kB]
Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf libpython2.7-minimal armhf 2.7.15~rc1-1 [334 kB]
Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf python2.7-minimal armhf 2.7.15~rc1-1 [1084 kB]
Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf python-minimal armhf 2.7.15~rc1-1 [28.1 kB]
Get:20 http://ftpmaster.internal/ubuntu bionic/main armhf libpython2.7-stdlib armhf 2.7.15~rc1-1 [1833 kB]
Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf python2.7 armhf 2.7.15~rc1-1 [238 kB]
Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libpython-stdlib armhf 2.7.15~rc1-1 [7624 B]
Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf python armhf 2.7.15~rc1-1 [140 kB]
Get:24 http://ftpmaster.internal/ubuntu bionic/main armhf libmagic-mgc armhf 1:5.32-2 [184 kB]
Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf libmagic1 armhf 1:5.32-2 [62.7 kB]
Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf file armhf 1:5.32-2 [21.5 kB]
Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf libglib2.0-0 armhf 2.56.1-2ubuntu1 [1014 kB]
Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf libicu60 armhf 60.2-3ubuntu3 [7797 kB]
Get:29 http://ftpmaster.internal/ubuntu bionic/main armhf libxml2 armhf 2.9.4+dfsg1-6.1ubuntu1 [567 kB]
Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf gettext-base armhf 0.19.8.1-6 [46.2 kB]
Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB]
Get:32 http://ftpmaster.internal/ubuntu bionic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB]
Get:33 http://ftpmaster.internal/ubuntu bionic/main armhf libkeyutils1 armhf 1.5.9-9.2ubuntu2 [7796 B]
Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB]
Get:35 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB]
Get:36 http://ftpmaster.internal/ubuntu bionic/main armhf libpsl5 armhf 0.19.1-5build1 [40.5 kB]
Get:37 http://ftpmaster.internal/ubuntu bionic/main armhf libsigsegv2 armhf 2.12-1 [14.0 kB]
Get:38 http://ftpmaster.internal/ubuntu bionic/main armhf m4 armhf 1.4.18-1 [181 kB]
Get:39 http://ftpmaster.internal/ubuntu bionic/main armhf autoconf all 2.69-11 [322 kB]
Get:40 http://ftpmaster.internal/ubuntu bionic/main armhf autotools-dev all 20180224.1 [39.6 kB]
Get:41 http://ftpmaster.internal/ubuntu bionic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB]
Get:42 http://ftpmaster.internal/ubuntu bionic/main armhf autopoint all 0.19.8.1-6 [412 kB]
Get:43 http://ftpmaster.internal/ubuntu bionic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-1 [34.1 kB]
Get:44 http://ftpmaster.internal/ubuntu bionic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-1 [136 kB]
Get:45 http://ftpmaster.internal/ubuntu bionic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-1 [24.1 kB]
Get:46 http://ftpmaster.internal/ubuntu bionic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-1 [76.5 kB]
Get:47 http://ftpmaster.internal/ubuntu bionic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-1 [47.2 kB]
Get:48 http://ftpmaster.internal/ubuntu bionic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-1 [87.9 kB]
Get:49 http://ftpmaster.internal/ubuntu bionic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-1 [168 kB]
Get:50 http://ftpmaster.internal/ubuntu bionic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-1 [13.1 kB]
Get:51 http://ftpmaster.internal/ubuntu bionic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-1 [78.8 kB]
Get:52 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.0 kB]
Get:53 http://ftpmaster.internal/ubuntu bionic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB]
Get:54 http://ftpmaster.internal/ubuntu bionic/main armhf libldap-common all 2.4.45+dfsg-1ubuntu1 [16.6 kB]
Get:55 http://ftpmaster.internal/ubuntu bionic/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1ubuntu1 [132 kB]
Get:56 http://ftpmaster.internal/ubuntu bionic/main armhf libnghttp2-14 armhf 1.30.0-1ubuntu1 [67.4 kB]
Get:57 http://ftpmaster.internal/ubuntu bionic/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [49.1 kB]
Get:58 http://ftpmaster.internal/ubuntu bionic/main armhf libcurl3-gnutls armhf 7.58.0-2ubuntu3 [182 kB]
Get:59 http://ftpmaster.internal/ubuntu bionic/universe armhf libhts2 armhf 1.7-2 [257 kB]
Get:60 http://ftpmaster.internal/ubuntu bionic/universe armhf bcftools armhf 1.7-2 [443 kB]
Get:61 http://ftpmaster.internal/ubuntu bionic/universe armhf cython armhf 0.26.1-0.4 [1773 kB]
Get:62 http://ftpmaster.internal/ubuntu bionic/universe armhf cython3 armhf 0.26.1-0.4 [1811 kB]
Get:63 http://ftpmaster.internal/ubuntu bionic/main armhf libtool all 2.4.6-2 [194 kB]
Get:64 http://ftpmaster.internal/ubuntu bionic/main armhf dh-autoreconf all 17 [15.8 kB]
Get:65 http://ftpmaster.internal/ubuntu bionic/main armhf libarchive-zip-perl all 1.60-1 [83.9 kB]
Get:66 http://ftpmaster.internal/ubuntu bionic/main armhf libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB]
Get:67 http://ftpmaster.internal/ubuntu bionic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB]
Get:68 http://ftpmaster.internal/ubuntu bionic/main armhf dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B]
Get:69 http://ftpmaster.internal/ubuntu bionic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB]
Get:70 http://ftpmaster.internal/ubuntu bionic/main armhf gettext armhf 0.19.8.1-6 [833 kB]
Get:71 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB]
Get:72 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB]
Get:73 http://ftpmaster.internal/ubuntu bionic/main armhf debhelper all 11.1.6ubuntu1 [902 kB]
Get:74 http://ftpmaster.internal/ubuntu bionic/main armhf python3-lib2to3 all 3.6.5-3 [76.6 kB]
Get:75 http://ftpmaster.internal/ubuntu bionic/main armhf python3-distutils all 3.6.5-3 [141 kB]
Get:76 http://ftpmaster.internal/ubuntu bionic/main armhf dh-python all 3.20180325ubuntu2 [89.2 kB]
Get:77 http://ftpmaster.internal/ubuntu bionic/main armhf libexpat1-dev armhf 2.2.5-3 [106 kB]
Get:78 http://ftpmaster.internal/ubuntu bionic/main armhf liblzma-dev armhf 5.2.2-1.3 [138 kB]
Get:79 http://ftpmaster.internal/ubuntu bionic/universe armhf libhts-dev armhf 1.7-2 [339 kB]
Get:80 http://ftpmaster.internal/ubuntu bionic/main armhf libpython2.7 armhf 2.7.15~rc1-1 [901 kB]
Get:81 http://ftpmaster.internal/ubuntu bionic/main armhf libpython2.7-dev armhf 2.7.15~rc1-1 [27.7 MB]
Get:82 http://ftpmaster.internal/ubuntu bionic/main armhf libpython-dev armhf 2.7.15~rc1-1 [7688 B]
Get:83 http://ftpmaster.internal/ubuntu bionic/main armhf libpython-all-dev armhf 2.7.15~rc1-1 [1092 B]
Get:84 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6 armhf 3.6.5-3 [1263 kB]
Get:85 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3.6-dev armhf 3.6.5-3 [2391 kB]
Get:86 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3-dev armhf 3.6.5-3 [7372 B]
Get:87 http://ftpmaster.internal/ubuntu bionic/main armhf libpython3-all-dev armhf 3.6.5-3 [1092 B]
Get:88 http://ftpmaster.internal/ubuntu bionic/main armhf python-all armhf 2.7.15~rc1-1 [1076 B]
Get:89 http://ftpmaster.internal/ubuntu bionic/main armhf python2.7-dev armhf 2.7.15~rc1-1 [287 kB]
Get:90 http://ftpmaster.internal/ubuntu bionic/main armhf python-dev armhf 2.7.15~rc1-1 [1256 B]
Get:91 http://ftpmaster.internal/ubuntu bionic/main armhf python-all-dev armhf 2.7.15~rc1-1 [1100 B]
Get:92 http://ftpmaster.internal/ubuntu bionic/main armhf python-attr all 17.4.0-2 [23.7 kB]
Get:93 http://ftpmaster.internal/ubuntu bionic/main armhf python-funcsigs all 1.0.2-4 [13.5 kB]
Get:94 http://ftpmaster.internal/ubuntu bionic/main armhf python-pkg-resources all 39.0.1-2 [128 kB]
Get:95 http://ftpmaster.internal/ubuntu bionic/universe armhf python-pluggy all 0.6.0-1 [12.2 kB]
Get:96 http://ftpmaster.internal/ubuntu bionic/universe armhf python-py all 1.5.2-1 [65.1 kB]
Get:97 http://ftpmaster.internal/ubuntu bionic/main armhf python-six all 1.11.0-2 [11.3 kB]
Get:98 http://ftpmaster.internal/ubuntu bionic/universe armhf python-pytest all 3.3.2-2 [142 kB]
Get:99 http://ftpmaster.internal/ubuntu bionic/main armhf python-setuptools all 39.0.1-2 [329 kB]
Get:100 http://ftpmaster.internal/ubuntu bionic/main armhf python3-all armhf 3.6.5-3 [1092 B]
Get:101 http://ftpmaster.internal/ubuntu bionic/main armhf python3.6-dev armhf 3.6.5-3 [512 kB]
Get:102 http://ftpmaster.internal/ubuntu bionic/main armhf python3-dev armhf 3.6.5-3 [1300 B]
Get:103 http://ftpmaster.internal/ubuntu bionic/main armhf python3-all-dev armhf 3.6.5-3 [1092 B]
Get:104 http://ftpmaster.internal/ubuntu bionic/main armhf python3-attr all 17.4.0-2 [23.8 kB]
Get:105 http://ftpmaster.internal/ubuntu bionic/main armhf python3-pkg-resources all 39.0.1-2 [98.8 kB]
Get:106 http://ftpmaster.internal/ubuntu bionic/universe armhf python3-pluggy all 0.6.0-1 [12.3 kB]
Get:107 http://ftpmaster.internal/ubuntu bionic/universe armhf python3-py all 1.5.2-1 [65.2 kB]
Get:108 http://ftpmaster.internal/ubuntu bionic/main armhf python3-six all 1.11.0-2 [11.4 kB]
Get:109 http://ftpmaster.internal/ubuntu bionic/universe armhf python3-pytest all 3.3.2-2 [142 kB]
Get:110 http://ftpmaster.internal/ubuntu bionic/main armhf python3-setuptools all 39.0.1-2 [248 kB]
Get:111 http://ftpmaster.internal/ubuntu bionic/universe armhf samtools armhf 1.7-1 [257 kB]
Get:112 http://ftpmaster.internal/ubuntu bionic/universe armhf tabix armhf 1.7-2 [270 kB]
Get:113 http://ftpmaster.internal/ubuntu bionic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB]
Get:114 http://ftpmaster.internal/ubuntu bionic/main armhf dh-exec armhf 0.23build1 [23.5 kB]
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up bcftools (1.7-2) ...
Setting up dh-autoreconf (17) ...
Setting up debhelper (11.1.6ubuntu1) ...
Setting up dh-strip-nondeterminism (0.040-1.1~build1) ...
Setting up dh-exec (0.23build1) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...

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

Kernel: Linux 4.4.0-121-generic arm64 (armv7l)
Toolchain package versions: binutils_2.30-15ubuntu1 dpkg-dev_1.19.0.5ubuntu2 g++-7_7.3.0-16ubuntu3 gcc-7_7.3.0-16ubuntu3 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-16ubuntu3 libstdc++6_8-20180414-1ubuntu2 linux-libc-dev_4.15.0-20.21
Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1ubuntu2 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 bcftools_1.7-2 binutils_2.30-15ubuntu1 binutils-arm-linux-gnueabihf_2.30-15ubuntu1 binutils-common_2.30-15ubuntu1 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2 cpp-7_7.3.0-16ubuntu3 cython_0.26.1-0.4 cython3_0.26.1-0.4 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu1 debianutils_4.8.4 dh-autoreconf_17 dh-exec_0.23build1 dh-python_3.20180325ubuntu2 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2 dpkg-dev_1.19.0.5ubuntu2 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2 g++-7_7.3.0-16ubuntu3 gcc_4:7.3.0-3ubuntu2 gcc-7_7.3.0-16ubuntu3 gcc-7-base_7.3.0-16ubuntu3 gcc-8-base_8-20180414-1ubuntu2 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-16ubuntu3 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8-20180414-1ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-15ubuntu1 libblkid1_2.31.1-0.4ubuntu3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1ubuntu2 libcilkrts5_7.3.0-16ubuntu3 libcom-err2_1.44.1-1 libcomerr2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcurl3-gnutls_7.58.0-2ubuntu3 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.3.0-16ubuntu3 libgcc1_1:8-20180414-1ubuntu2 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8-20180414-1ubuntu2 libgpg-error0_1.27-6 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu2 libkmod2_24-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 libldap-2.4-2_2.4.45+dfsg-1ubuntu1 libldap-common_2.4.45+dfsg-1ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.4ubuntu3 libmpc3_1.1.0-1 libmpdec2_2.4.2-1ubuntu1 libmpfr6_4.0.1-1 libncurses5_6.1-1ubuntu1 libncursesw5_6.1-1ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu1 libpsl5_0.19.1-5build1 libpython-all-dev_2.7.15~rc1-1 libpython-dev_2.7.15~rc1-1 libpython-stdlib_2.7.15~rc1-1 libpython2.7_2.7.15~rc1-1 libpython2.7-dev_2.7.15~rc1-1 libpython2.7-minimal_2.7.15~rc1-1 libpython2.7-stdlib_2.7.15~rc1-1 libpython3-all-dev_3.6.5-3 libpython3-dev_3.6.5-3 libpython3-stdlib_3.6.5-3 libpython3.6_3.6.5-3 libpython3.6-dev_3.6.5-3 libpython3.6-minimal_3.6.5-3 libpython3.6-stdlib_3.6.5-3 libreadline7_7.0-3 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1 libssl1.1_1.1.0g-2ubuntu4 libstdc++-7-dev_7.3.0-16ubuntu3 libstdc++6_8-20180414-1ubuntu2 libsystemd0_237-3ubuntu10 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1 libtool_2.4.6-2 libubsan0_7.3.0-16ubuntu3 libudev1_237-3ubuntu10 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libuuid1_2.31.1-0.4ubuntu3 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-20.21 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.31.1-0.4ubuntu3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1 ncurses-bin_6.1-1ubuntu1 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6 perl-base_5.26.1-6 perl-modules-5.26_5.26.1-6 pinentry-curses_1.1.0-1 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1 python_2.7.15~rc1-1 python-all_2.7.15~rc1-1 python-all-dev_2.7.15~rc1-1 python-attr_17.4.0-2 python-dev_2.7.15~rc1-1 python-funcsigs_1.0.2-4 python-minimal_2.7.15~rc1-1 python-pkg-resources_39.0.1-2 python-pluggy_0.6.0-1 python-py_1.5.2-1 python-pytest_3.3.2-2 python-setuptools_39.0.1-2 python-six_1.11.0-2 python2.7_2.7.15~rc1-1 python2.7-dev_2.7.15~rc1-1 python2.7-minimal_2.7.15~rc1-1 python3_3.6.5-3 python3-all_3.6.5-3 python3-all-dev_3.6.5-3 python3-attr_17.4.0-2 python3-dev_3.6.5-3 python3-distutils_3.6.5-3 python3-lib2to3_3.6.5-3 python3-minimal_3.6.5-3 python3-pkg-resources_39.0.1-2 python3-pluggy_0.6.0-1 python3-py_1.5.2-1 python3-pytest_3.3.2-2 python3-setuptools_39.0.1-2 python3-six_1.11.0-2 python3.6_3.6.5-3 python3.6-dev_3.6.5-3 python3.6-minimal_3.6.5-3 readline-common_7.0-3 samtools_1.7-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10 systemd-sysv_237-3ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tabix_1.7-2 tar_1.29b-2 tzdata_2018d-1 ubuntu-keyring_2018.02.28 util-linux_2.31.1-0.4ubuntu3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2

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


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

gpgv: Signature made Mon Feb 19 10:25:07 2018 UTC
gpgv:                using RSA key AFCFEC8E669CE1C2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.14+ds-2.dsc
dpkg-source: info: extracting python-pysam in python-pysam-0.14+ds
dpkg-source: info: unpacking python-pysam_0.14+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.14+ds-2.debian.tar.xz
dpkg-source: info: applying execute-linking-tests-only-when-explicitely-reque.patch
dpkg-source: info: applying xfail.patch
dpkg-source: info: applying exclude_tests_accessing_remote_http.patch
dpkg-source: info: applying skip_test_needing_missing_data.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=noautodbgsym parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-14618406
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14618406
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-14618406
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

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

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.14+ds-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build python-pysam-0.14+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-0.14+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-0.14+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
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-0.14+ds'
dh_auto_clean
I: pybuild base:217: 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-0.14+ds/.pybuild/cpython2_2.7_pysam/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:217: 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-0.14+ds/.pybuild/cpython3_3.6_pysam/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
rm -f \
	pysam/config.py \
	pysam/config.h \
	pysam/lib*.c \
	samtools/config.h \
	bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
   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:217: 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:217: 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
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /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-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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,-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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
creating build/temp.linux-armhf-2.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:54:66: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, samtools_stdout) & fputc('\n', samtools_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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-2.7/samtools/lz4/lz4.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,-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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.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_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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/htslib/kstring.h:29:0,
                 from /usr/include/htslib/vcf.h:40,
                 from bcftools/vcfcall.c.pysam.c:34:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:539:14: 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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.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/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:10866:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5595:7: 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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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,-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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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 -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29407:126: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ^
In file included from pysam/htslib_util.h:4:0,
                 from pysam/libcalignmentfile.c:490:
/usr/include/htslib/sam.h:594:9: note: expected ‘const bam_pileup1_t ** {aka const struct <anonymous> **}’ but argument is of type ‘bam_pileup1_t ** {aka struct <anonymous> **}’
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
         ^~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27655:9: 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:13792:13: 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_hdr);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14127:3: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
   sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8638:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13932:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 965, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13964:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 966, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14341:43: warning: overflow in implicit constant conversion [-Woverflow]
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 995, __pyx_L1_error)
                                           ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:32913:3: 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:489:
/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,-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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.69’:
pysam/libcvcf.c:24705:16: 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,-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-DsmO56/python2.7-2.7.15~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /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-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libchtslib.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
creating build/temp.linux-armhf-3.6/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.6/samtools/samtools.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:54:66: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, samtools_stdout) & fputc('\n', samtools_stdout) != EOF) ret = 0;
                                                                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.6/samtools/lz4/lz4.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,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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_cat.c.pysam.o build/temp.linux-armhf-3.6/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.6/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.6/samtools/phase.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.6/samtools/sample.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam.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_utils.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/samtools.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.6/samtools/dict.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/padding.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.6/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bcftools.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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/vcfconcat.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.6/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfannotate.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/bam_sample.c.pysam.o build/temp.linux-armhf-3.6/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.6/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.6/bcftools/main.c.pysam.o build/temp.linux-armhf-3.6/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.6/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.6/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.6/bcftools/em.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfindex.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:304:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5595:7: 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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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 -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcutils.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:29407:126: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ^
In file included from pysam/htslib_util.h:4:0,
                 from pysam/libcalignmentfile.c:490:
/usr/include/htslib/sam.h:594:9: note: expected ‘const bam_pileup1_t ** {aka const struct <anonymous> **}’ but argument is of type ‘bam_pileup1_t ** {aka struct <anonymous> **}’
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
         ^~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27655:9: 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:13792:13: 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_hdr);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignmentfile.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamfile.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14127:3: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
   sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:8638:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13932:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 965, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13964:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 966, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14341:43: warning: overflow in implicit constant conversion [-Woverflow]
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 995, __pyx_L1_error)
                                           ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabix.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcfaidx.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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:32913:3: 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:489:
/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,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbgzf.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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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 -Wl,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -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.71’:
pysam/libcvcf.c:24705:16: 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,-Bsymbolic-functions -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+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-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcvcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+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 calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view -bS with_md.sam > with_md.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS tag_bug.sam > tag_bug.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 test_unaligned.sam > test_unaligned.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 ex4.sam > ex4.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 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 ex6.sam > ex6.bam
samtools view -bS example_user_header.sam > example_user_header.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index ex9_nofail.bam
samtools index tag_bug.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index test_unaligned.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index ex4.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.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 ex6.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+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 < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf gnomad_fixed.vcf.gz    # create tbi index
bcftools index gnomad_fixed.vcf.gz  # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz    # create tbi index
bcftools index gnomad.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 gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.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-0.14+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:217: cd /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
============================= test session starts ==============================
platform linux2 -- Python 2.7.15rc1, pytest-3.3.2, py-1.5.2, pluggy-0.6.0 -- /usr/bin/python2.7
cachedir: ../../../.cache
rootdir: /<<BUILDDIR>>/python-pysam-0.14+ds, inifile: setup.cfg
collecting ... collected 908 items

tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED      [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED     [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED       [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED     [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED   [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED  [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED   [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED [  0%]
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED      [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED     [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED  [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED [  1%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED [  2%]
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED [  2%]
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED [  3%]
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED [  4%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED [  5%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED [  5%]
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED [  5%]
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED                [  5%]
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED          [  5%]
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED           [  5%]
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED [  5%]
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED               [  5%]
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED           [  5%]
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED             [  6%]
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED              [  6%]
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED              [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED          [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED        [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED       [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED        [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED      [  6%]
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED     [  6%]
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED            [  7%]
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED      [  7%]
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED [  7%]
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED                [  7%]
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED            [  7%]
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED     [  7%]
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED                  [  7%]
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED              [  7%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED [  7%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection FAILED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED [  8%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection FAILED [  9%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED [ 10%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED [ 10%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED [ 10%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED [ 10%]
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED [ 10%]
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED [ 10%]
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED [ 10%]
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED [ 10%]
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED [ 10%]
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED [ 11%]
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED [ 11%]
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED [ 11%]
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED [ 11%]
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED  [ 11%]
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED [ 11%]
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED [ 11%]
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED [ 11%]
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED [ 11%]
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED [ 12%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED [ 13%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED [ 14%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM PASSED  [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM PASSED [ 15%]
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM PASSED  [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED [ 16%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED [ 17%]
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED   [ 18%]
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED [ 18%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED [ 19%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED [ 19%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED [ 19%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED [ 19%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED [ 19%]
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED [ 19%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED [ 19%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED   [ 19%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED [ 19%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED    [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED    [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED    [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED    [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED     [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED   [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED   [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED    [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED   [ 20%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED   [ 21%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED     [ 21%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED       [ 21%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED [ 21%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED [ 21%]
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED      [ 21%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED [ 21%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED   [ 21%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED [ 21%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED    [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED    [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED    [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED    [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED     [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED   [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED   [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED    [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED   [ 22%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED   [ 23%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED     [ 23%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED       [ 23%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED [ 23%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED [ 23%]
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED      [ 23%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength PASSED [ 23%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar PASSED  [ 23%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring PASSED [ 23%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag PASSED   [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq PASSED   [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos PASSED   [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm PASSED   [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos PASSED    [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname PASSED  [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual PASSED  [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual PASSED   [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery PASSED  [ 24%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname PASSED  [ 25%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq PASSED    [ 25%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt PASSED      [ 25%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags PASSED     [ 25%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED [ 25%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED  [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED [ 26%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED  [ 27%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED    [ 27%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED   [ 27%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag PASSED [ 27%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname PASSED [ 28%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt PASSED   [ 29%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags PASSED  [ 29%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED [ 29%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED  [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED [ 30%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED  [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED    [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED   [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED    [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED     [ 31%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED     [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED     [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED     [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED      [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED    [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED    [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED     [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED    [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED    [ 32%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED      [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED        [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED       [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED  [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED   [ 33%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED   [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED   [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED   [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED    [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED  [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED  [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED   [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED  [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED  [ 34%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED    [ 35%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED      [ 35%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED [ 35%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED [ 35%]
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED     [ 35%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED [ 35%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED    [ 35%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED [ 35%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED     [ 35%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED     [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED     [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED     [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED      [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED    [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED    [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED     [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED    [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED    [ 36%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED      [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED        [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED       [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED  [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED   [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED   [ 37%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED   [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED   [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED    [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED  [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED  [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED   [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED  [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED  [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED    [ 38%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED      [ 39%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED [ 39%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED [ 39%]
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED     [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength PASSED [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar PASSED   [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring PASSED [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag PASSED    [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq PASSED    [ 39%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos PASSED    [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm PASSED    [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos PASSED     [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname PASSED   [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual PASSED   [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual PASSED    [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery PASSED   [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname PASSED   [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq PASSED     [ 40%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt PASSED       [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools PASSED [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields PASSED [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags PASSED      [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength PASSED [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar PASSED [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring PASSED [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag PASSED  [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq PASSED  [ 41%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos PASSED  [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm PASSED  [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos PASSED   [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname PASSED [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual PASSED [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual PASSED  [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery PASSED [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname PASSED [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq PASSED   [ 42%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt PASSED     [ 43%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags PASSED    [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED [ 43%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED  [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED  [ 44%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED    [ 45%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED [ 45%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED [ 45%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED [ 45%]
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED   [ 45%]
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED                  [ 45%]
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM PASSED                 [ 45%]
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED                  [ 45%]
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED          [ 45%]
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED          [ 46%]
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED [ 46%]
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM PASSED                 [ 46%]
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM <- ../../../usr/lib/python2.7/unittest/case.py PASSED [ 46%]
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM PASSED                 [ 46%]
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED                 [ 46%]
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED       [ 46%]
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED      [ 46%]
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED [ 46%]
tests/AlignmentFile_test.py::TestIO::testHead PASSED                     [ 47%]
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED         [ 47%]
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED [ 47%]
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED [ 47%]
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED [ 47%]
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED                  [ 47%]
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM PASSED                 [ 47%]
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED                  [ 47%]
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED     [ 47%]
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED            [ 48%]
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED [ 48%]
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam
PASSED [ 49%]
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED              [ 49%]
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM PASSED             [ 49%]
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED              [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED   [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig PASSED [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges PASSED [ 49%]
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig PASSED [ 50%]
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges PASSED [ 50%]
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED     [ 50%]
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED  [ 50%]
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED           [ 50%]
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED [ 50%]
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED [ 50%]
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED [ 50%]
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED [ 50%]
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED      [ 50%]
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED        [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED  [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
[E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
PASSED      [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED [ 51%]
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED [ 52%]
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED       [ 52%]
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED    [ 52%]
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED  [ 52%]
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED  [ 52%]
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED    [ 52%]
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED [ 52%]
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED [ 52%]
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED [ 52%]
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED [ 53%]
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED     [ 53%]
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED [ 53%]
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes
PASSED  [ 53%]
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED            [ 53%]
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED       [ 53%]
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED            [ 53%]
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED       [ 53%]
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED  [ 53%]
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue PASSED [ 54%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch PASSED [ 55%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF PASSED [ 55%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue PASSED [ 55%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse PASSED [ 55%]
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue PASSED [ 55%]
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED          [ 55%]
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED          [ 55%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED [ 55%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED [ 55%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED [ 56%]
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED [ 56%]
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED            [ 56%]
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED          [ 56%]
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED          [ 57%]
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED               [ 57%]
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED             [ 57%]
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED             [ 57%]
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED [ 57%]
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED [ 57%]
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED [ 57%]
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED [ 57%]
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED [ 57%]
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED         [ 58%]
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file
PASSED          [ 58%]
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file
PASSED          [ 58%]
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED    [ 58%]
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED [ 58%]
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED [ 58%]
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED [ 58%]
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED         [ 58%]
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED [ 58%]
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED      [ 59%]
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED [ 59%]
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram PASSED [ 59%]
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED [ 59%]
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED [ 59%]
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED [ 59%]
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED          [ 59%]
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED        [ 59%]
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED            [ 59%]
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED          [ 60%]
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED       [ 60%]
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED     [ 60%]
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED             [ 60%]
tests/VariantFile_test.py::TestOpening::testDetectVCF [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.)
PASSED             [ 60%]
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED           [ 60%]
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED          [ 60%]
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED [ 60%]
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED [ 60%]
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED [ 61%]
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED [ 61%]
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf
PASSED           [ 61%]
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz
PASSED      [ 61%]
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED [ 61%]
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED [ 61%]
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED [ 61%]
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED [ 61%]
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED [ 61%]
tests/VariantFile_test.py::TestHeader::testIterator PASSED               [ 62%]
tests/VariantFile_test.py::TestHeader::testStr PASSED                    [ 62%]
tests/VariantFile_test.py::TestParsing::testAlleles PASSED               [ 62%]
tests/VariantFile_test.py::TestParsing::testAlt PASSED                   [ 62%]
tests/VariantFile_test.py::TestParsing::testChrom PASSED                 [ 62%]
tests/VariantFile_test.py::TestParsing::testFilter PASSED                [ 62%]
tests/VariantFile_test.py::TestParsing::testFormat PASSED                [ 62%]
tests/VariantFile_test.py::TestParsing::testId PASSED                    [ 62%]
tests/VariantFile_test.py::TestParsing::testInfo PASSED                  [ 62%]
tests/VariantFile_test.py::TestParsing::testPos PASSED                   [ 62%]
tests/VariantFile_test.py::TestParsing::testQual PASSED                  [ 63%]
tests/VariantFile_test.py::TestParsing::testRef PASSED                   [ 63%]
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED   [ 63%]
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED         [ 63%]
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED         [ 63%]
tests/VariantFile_test.py::TestParsing::testStart PASSED                 [ 63%]
tests/VariantFile_test.py::TestParsing::testStop PASSED                  [ 63%]
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED            [ 63%]
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED [ 63%]
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED [ 64%]
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED [ 65%]
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED [ 65%]
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED      [ 65%]
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
FAILED  [ 65%]
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED   [ 65%]
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED         [ 65%]
tests/compile_test.py::BAMTest::testCount PASSED                         [ 65%]
tests/compile_test.py::GTFTest::testCount PASSED                         [ 65%]
tests/faidx_test.py::TestFastaFile::testFetch PASSED                     [ 65%]
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED               [ 66%]
tests/faidx_test.py::TestFastaFile::testLength PASSED                    [ 66%]
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED          [ 66%]
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED           [ 66%]
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED [ 66%]
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED [ 66%]
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED [ 66%]
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED [ 66%]
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED [ 66%]
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED [ 67%]
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED [ 67%]
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED [ 67%]
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED               [ 67%]
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED              [ 67%]
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED          [ 67%]
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED             [ 67%]
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED               [ 67%]
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED              [ 67%]
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED          [ 68%]
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED             [ 68%]
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED               [ 68%]
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED              [ 68%]
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED          [ 68%]
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED             [ 68%]
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED         [ 68%]
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED        [ 68%]
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED    [ 68%]
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED       [ 69%]
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED [ 69%]
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED               [ 69%]
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED [ 69%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED [ 70%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED [ 70%]
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED [ 70%]
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED [ 70%]
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED [ 70%]
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED [ 70%]
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED [ 70%]
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED [ 70%]
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED [ 70%]
tests/samtools_test.py::SamtoolsTest::testStatements PASSED              [ 71%]
tests/samtools_test.py::SamtoolsTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED [ 71%]
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED            [ 71%]
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED       [ 71%]
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED     [ 71%]
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED             [ 71%]
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED                [ 71%]
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED      [ 71%]
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED   [ 71%]
tests/samtools_test.py::PysamTest::testStatements PASSED                 [ 72%]
tests/samtools_test.py::PysamTest::testUsage <- ../../../usr/lib/python2.7/unittest/case.py SKIPPED [ 72%]
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED             [ 72%]
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED                [ 72%]
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED                 [ 72%]
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED                [ 72%]
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED                 [ 72%]
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED                [ 72%]
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED [ 72%]
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED  [ 73%]
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED                 [ 73%]
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED                [ 73%]
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED                 [ 73%]
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED                [ 73%]
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED                 [ 73%]
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED                [ 73%]
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED                 [ 73%]
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED                [ 73%]
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED [ 74%]
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED  [ 74%]
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED     [ 74%]
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [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
PASSED        [ 74%]
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED             [ 74%]
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED                [ 74%]
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED           [ 74%]
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED          [ 74%]
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED     [ 74%]
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [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
PASSED        [ 75%]
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED     [ 75%]
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED        [ 75%]
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED     [ 75%]
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [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
PASSED        [ 75%]
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED                [ 75%]
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED               [ 75%]
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED                [ 75%]
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED               [ 75%]
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED                [ 75%]
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED               [ 76%]
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED                [ 76%]
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED               [ 76%]
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED                [ 76%]
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED               [ 76%]
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED                [ 76%]
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED               [ 76%]
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED                [ 76%]
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED               [ 76%]
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED                [ 77%]
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED               [ 77%]
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED                 [ 77%]
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED                [ 77%]
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED             [ 77%]
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED                [ 77%]
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED             [ 77%]
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED                [ 77%]
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED     [ 77%]
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [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.)
PASSED        [ 78%]
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED     [ 78%]
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [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
PASSED        [ 78%]
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED             [ 78%]
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED                [ 78%]
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED       [ 78%]
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED          [ 78%]
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED             [ 78%]
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED                [ 78%]
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED             [ 79%]
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED                [ 79%]
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED     [ 79%]
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED        [ 79%]
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED                [ 79%]
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED               [ 79%]
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED             [ 79%]
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED                [ 79%]
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED           [ 79%]
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED          [ 80%]
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED                [ 80%]
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED               [ 80%]
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED                [ 80%]
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED               [ 80%]
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED                [ 80%]
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED               [ 80%]
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED                 [ 80%]
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED                [ 80%]
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED            [ 81%]
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED               [ 81%]
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED            [ 81%]
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED               [ 81%]
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED            [ 81%]
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED               [ 81%]
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED            [ 81%]
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED               [ 81%]
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED            [ 81%]
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED               [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED    [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [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.)
PASSED       [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED    [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED       [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED    [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED       [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED    [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED       [ 82%]
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED     [ 83%]
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [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
PASSED        [ 83%]
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED    [ 83%]
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED       [ 83%]
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED    [ 83%]
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [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.)
PASSED       [ 83%]
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED            [ 83%]
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED               [ 83%]
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED            [ 83%]
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED               [ 84%]
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED            [ 84%]
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED               [ 84%]
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED            [ 84%]
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED               [ 84%]
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED            [ 84%]
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED               [ 84%]
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED            [ 84%]
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED               [ 84%]
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED    [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [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
PASSED       [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED    [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [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
PASSED       [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED    [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [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.)
PASSED       [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED    [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [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.)
PASSED       [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED    [ 85%]
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [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
PASSED       [ 86%]
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED            [ 86%]
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED               [ 86%]
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED       [ 86%]
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED          [ 86%]
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED    [ 86%]
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [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
PASSED       [ 86%]
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED [ 86%]
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED [ 86%]
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED [ 87%]
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED [ 87%]
tests/tabix_test.py::TestCompression::testCompression PASSED             [ 87%]
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED   [ 87%]
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED [ 87%]
tests/tabix_test.py::TestCompressionSam::testCompression PASSED          [ 87%]
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED [ 87%]
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED [ 87%]
tests/tabix_test.py::TestCompressionBed::testCompression PASSED          [ 87%]
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED [ 87%]
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED [ 88%]
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED          [ 88%]
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED [ 88%]
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED [ 88%]
tests/tabix_test.py::TestGZFile::testAll PASSED                          [ 88%]
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED        [ 88%]
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED [ 88%]
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED     [ 88%]
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED [ 88%]
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED  [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED [ 89%]
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED  [ 89%]
tests/tabix_test.py::TestIterationWithComments::testAll PASSED           [ 89%]
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED    [ 89%]
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED        [ 90%]
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED [ 90%]
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED     [ 90%]
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED    [ 90%]
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED [ 90%]
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED [ 90%]
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED   [ 90%]
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED [ 90%]
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED     [ 90%]
tests/tabix_test.py::TestIterators::testClosedFile PASSED                [ 91%]
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED       [ 91%]
tests/tabix_test.py::TestIterators::testIteration PASSED                 [ 91%]
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED [ 91%]
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED [ 91%]
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED [ 91%]
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED  [ 91%]
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED [ 91%]
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED   [ 91%]
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED [ 92%]
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED [ 92%]
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED [ 92%]
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED [ 92%]
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED [ 92%]
tests/tabix_test.py::TestBed::testRead PASSED                            [ 92%]
tests/tabix_test.py::TestBed::testWrite PASSED                           [ 92%]
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED                   [ 92%]
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED                  [ 92%]
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED               [ 93%]
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED                  [ 93%]
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED       [ 93%]
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [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.)
PASSED          [ 93%]
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED              [ 93%]
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED [ 93%]
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED          [ 93%]
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED      [ 93%]
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED      [ 93%]
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED        [ 94%]
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED          [ 94%]
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED      [ 94%]
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED      [ 94%]
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED [ 94%]
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED       [ 94%]
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED   [ 94%]
tests/tabix_test.py::TestMultipleIterators::testScope PASSED             [ 94%]
tests/tabix_test.py::TestContextManager::testManager PASSED              [ 94%]
tests/tabixproxies_test.py::TestParser::testCopy PASSED                  [ 95%]
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED    [ 95%]
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED  [ 95%]
tests/tabixproxies_test.py::TestParser::testRead PASSED                  [ 95%]
tests/tabixproxies_test.py::TestParser::testUnset PASSED                 [ 95%]
tests/tabixproxies_test.py::TestParser::testWrite PASSED                 [ 95%]
tests/tabixproxies_test.py::TestGTF::testCopy PASSED                     [ 95%]
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED       [ 95%]
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED     [ 95%]
tests/tabixproxies_test.py::TestGTF::testRead PASSED                     [ 96%]
tests/tabixproxies_test.py::TestGTF::testUnset PASSED                    [ 96%]
tests/tabixproxies_test.py::TestGTF::testWrite PASSED                    [ 96%]
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED [ 96%]
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED  [ 96%]
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED [ 96%]
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED [ 96%]
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED [ 96%]
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED [ 96%]
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED          [ 97%]
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED [ 97%]
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED [ 97%]
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED [ 97%]
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED [ 97%]
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED [ 97%]
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED                    [ 97%]
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED      [ 97%]
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED    [ 97%]
tests/tabixproxies_test.py::TestGFF3::testRead PASSED                    [ 98%]
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED                   [ 98%]
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED                   [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED [ 98%]
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED         [ 99%]
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED [ 99%]
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED [ 99%]
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED [ 99%]
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED [ 99%]
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED [ 99%]
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED    [ 99%]
tests/test_samtools_python.py::test_bedcov_split_lines PASSED            [ 99%]
tests/test_samtools_python.py::test_idxstats_parse PASSED                [ 99%]
tests/test_samtools_python.py::test_bedcov PASSED                        [100%]

=================================== FAILURES ===================================
_________ TestSetTagGetTag.test_set_tag_with_automated_type_detection __________

self = <AlignedSegment_test.TestSetTagGetTag testMethod=test_set_tag_with_automated_type_detection>

    def test_set_tag_with_automated_type_detection(self):
        self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
        self.check_tag('TT', -(1 << 7) - 1,
                       value_type=None, alt_value_type="s")
        self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
        self.check_tag('TT', -(1 << 15) - 1,
                       value_type=None, alt_value_type="i")
>       self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")

tests/AlignedSegment_test.py:1148: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignedSegment_test.py:1099: in check_tag
    a.set_tag(tag, value, value_type=value_type)
pysam/libcalignedsegment.pyx:2214: in pysam.libcalignedsegment.AlignedSegment.set_tag
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   ValueError: can't guess type or invalid type code specified: -2147483648 None

pysam/libcalignedsegment.pyx:2293: ValueError
_________ TestSetTagsGetTag.test_set_tag_with_automated_type_detection _________

self = <AlignedSegment_test.TestSetTagsGetTag testMethod=test_set_tag_with_automated_type_detection>

    def test_set_tag_with_automated_type_detection(self):
        self.check_tag('TT', -(1 << 7), value_type=None, alt_value_type="c")
        self.check_tag('TT', -(1 << 7) - 1,
                       value_type=None, alt_value_type="s")
        self.check_tag('TT', -(1 << 15), value_type=None, alt_value_type="s")
        self.check_tag('TT', -(1 << 15) - 1,
                       value_type=None, alt_value_type="i")
>       self.check_tag('TT', -(1 << 31), value_type=None, alt_value_type="i")

tests/AlignedSegment_test.py:1148: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignedSegment_test.py:1177: in check_tag
    a.set_tags([(tag, value, value_type)])
pysam/libcalignedsegment.pyx:2559: in pysam.libcalignedsegment.AlignedSegment.set_tags
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   ValueError: could not deduce typecode for value -2147483648

pysam/libcalignedsegment.pyx:415: ValueError
_____________________ TestSettingRecordValues.testGenotype _____________________

self = <VariantFile_test.TestSettingRecordValues testMethod=testGenotype>

    def testGenotype(self):
        with pysam.VariantFile(os.path.join(CBCF_DATADIR, self.filename)) as inf:
            record = next(inf)
            sample = record.samples["NA00001"]
            print(sample["GT"])
            self.assertEqual(sample["GT"], (0, 0))
>           sample["GT"] = sample["GT"]

tests/VariantFile_test.py:592: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pysam/libcbcf.pyx:3442: in pysam.libcbcf.VariantRecordSample.__setitem__
    ???
pysam/libcbcf.pyx:855: in pysam.libcbcf.bcf_format_set_value
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>   ???
E   TypeError: invalid value for Integer format

pysam/libcbcf.pyx:588: TypeError
=============================== warnings summary ===============================
.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2
  /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1395: UserWarning: no BGZF EOF marker; file may be truncated
    ignore_truncation=True)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
======== 3 failed, 889 passed, 16 skipped, 1 warnings in 124.90 seconds ========
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13
debian/rules:31: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
debian/rules:24: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 20180427-0927

Finished
--------

E: Build failure (dpkg-buildpackage died)

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

Purging /<<BUILDDIR>>
Not removing build depends: as requested

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

Build Architecture: armhf
Build-Space: 131044
Build-Time: 1125
Distribution: bionic
Fail-Stage: build
Host Architecture: armhf
Install-Time: 50
Job: python-pysam_0.14+ds-2.dsc
Machine Architecture: arm64
Package: python-pysam
Package-Time: 1177
Source-Version: 0.14+ds-2
Space: 131044
Status: attempted
Version: 0.14+ds-2
--------------------------------------------------------------------------------
Finished at 20180427-0927
Build needed 00:19:37, 131044k disc space
RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406
Scanning for processes to kill in build PACKAGEBUILD-14618406
RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406
Stopping target for build PACKAGEBUILD-14618406
RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-14618406
Removing build PACKAGEBUILD-14618406