Raspbian Package Auto-Building

Build log for python-pysam (0.8.4+ds-1) on armhf

python-pysam → 0.8.4+ds-1 → armhf → 2015-11-19 07:36:43 

sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02

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║ python-pysam 0.8.4+ds-1 (armhf)                            19 Nov 2015 05:56 ║
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Package: python-pysam
Version: 0.8.4+ds-1
Source Version: 0.8.4+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/python-pysam-sHAb1v/python-pysam-0.8.4+ds' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/python-pysam-sHAb1v' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-c77d0fb5-cd60-4e28-8d74-c6e26715144c' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8472 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.4 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 18.9 MB in 34s (542 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
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Checking available source versions...

Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/python-pysam.git
Need to get 1815 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main python-pysam 0.8.4+ds-1 (dsc) [2404 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main python-pysam 0.8.4+ds-1 (tar) [1805 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main python-pysam 0.8.4+ds-1 (diff) [8068 B]
Fetched 1815 kB in 0s (4114 kB/s)
Download complete and in download only mode

Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-9Ri27I/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ 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
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
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After this operation, 0 B of additional disk space will be used.
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(Reading database ... 12953 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-python, samtools (>= 1.2), libhts-dev (>= 1.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python-nose, python3-all-dev, python3-setuptools, cython3 (>= 0.23), python3-nose
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-python, samtools (>= 1.2), libhts-dev (>= 1.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python-nose, python3-all-dev, python3-setuptools, cython3 (>= 0.23), python3-nose
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/«BUILDDIR»/resolver-91r_nG/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
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 extra packages will be installed:
  bsdmainutils cython cython3 debhelper dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libcroco3 libexpat1 libexpat1-dev libffi6 libfile-stripnondeterminism-perl
  libglib2.0-0 libhts-dev libhts1 libicu55 libmagic1 libmpdec2 libpipeline1
  libpython-all-dev libpython-dev libpython-stdlib libpython2.7
  libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
  libpython3-dev libpython3-stdlib libpython3.4 libpython3.4-dev
  libpython3.4-minimal libpython3.4-stdlib libpython3.5 libpython3.5-dev
  libpython3.5-minimal libpython3.5-stdlib libsqlite3-0 libssl1.0.2
  libunistring0 libxml2 man-db mime-support po-debconf python python-all
  python-all-dev python-dev python-minimal python-nose python-pkg-resources
  python-setuptools python2.7 python2.7-dev python2.7-minimal python3
  python3-all python3-all-dev python3-dev python3-minimal python3-nose
  python3-pkg-resources python3-setuptools python3.4 python3.4-dev
  python3.4-minimal python3.5 python3.5-dev python3.5-minimal samtools
  zlib1g-dev
Suggested packages:
  wamerican wordlist whois vacation cython-doc dh-make gettext-doc autopoint
  libasprintf-dev libgettextpo-dev groff less www-browser libmail-box-perl
  python-doc python-tk python-coverage python-nose-doc python-setuptools-doc
  python2.7-doc binfmt-support python3-doc python3-tk python3-venv
  python3.4-venv python3.4-doc python3.5-venv python3.5-doc
Recommended packages:
  curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
  libmail-sendmail-perl
The following NEW packages will be installed:
  bsdmainutils cython cython3 debhelper dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libcroco3 libexpat1 libexpat1-dev libffi6 libfile-stripnondeterminism-perl
  libglib2.0-0 libhts-dev libhts1 libicu55 libmagic1 libmpdec2 libpipeline1
  libpython-all-dev libpython-dev libpython-stdlib libpython2.7
  libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev
  libpython3-dev libpython3-stdlib libpython3.4 libpython3.4-dev
  libpython3.4-minimal libpython3.4-stdlib libpython3.5 libpython3.5-dev
  libpython3.5-minimal libpython3.5-stdlib libsqlite3-0 libssl1.0.2
  libunistring0 libxml2 man-db mime-support po-debconf python python-all
  python-all-dev python-dev python-minimal python-nose python-pkg-resources
  python-setuptools python2.7 python2.7-dev python2.7-minimal python3
  python3-all python3-all-dev python3-dev python3-minimal python3-nose
  python3-pkg-resources python3-setuptools python3.4 python3.4-dev
  python3.4-minimal python3.5 python3.5-dev python3.5-minimal samtools
  sbuild-build-depends-python-pysam-dummy zlib1g-dev
0 upgraded, 77 newly installed, 0 to remove and 2 not upgraded.
Need to get 136 MB/136 MB of archives.
After this operation, 279 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-3 [1084 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-5+b1 [380 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-5+b1 [1092 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.59 [36.4 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.9.2-1 [404 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libssl1.0.2 armhf 1.0.2d-3 [881 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-5+b1 [1811 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-5+b1 [265 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libmpdec2 armhf 2.4.1-1 [65.8 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libpython3.4-minimal armhf 3.4.3-10+b1 [493 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main python3.4-minimal armhf 3.4.3-10+b1 [1266 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main python3-minimal armhf 3.4.3-7 [35.1 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libpython3.4-stdlib armhf 3.4.3-10+b1 [2055 kB]
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Get:33 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main cython armhf 0.23.2+git16-ga8fbae1-1 [1444 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main cython3 armhf 0.23.2+git16-ga8fbae1-1 [1450 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:45 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-7 [114 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libhts1 armhf 1.2.1-1+rpi1 [190 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libhts-dev armhf 1.2.1-1+rpi1 [237 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main libpython2.7-dev armhf 2.7.10-5+b1 [27.1 MB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libpython-dev armhf 2.7.9-1 [19.6 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libpython-all-dev armhf 2.7.9-1 [1012 B]
Get:52 http://172.17.0.1/private/ stretch-staging/main libpython3.4 armhf 3.4.3-10+b1 [1094 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libpython3.4-dev armhf 3.4.3-10+b1 [33.5 MB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libpython3-dev armhf 3.4.3-7 [18.5 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libpython3.5-stdlib armhf 3.5.0-3+rpi1+b1 [2009 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libpython3.5 armhf 3.5.0-3+rpi1+b1 [1159 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libpython3.5-dev armhf 3.5.0-3+rpi1+b1 [36.5 MB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libpython3-all-dev armhf 3.4.3-7 [970 B]
Get:59 http://172.17.0.1/private/ stretch-staging/main python-all armhf 2.7.9-1 [994 B]
Get:60 http://172.17.0.1/private/ stretch-staging/main python2.7-dev armhf 2.7.10-5+b1 [279 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main python-dev armhf 2.7.9-1 [1188 B]
Get:62 http://172.17.0.1/private/ stretch-staging/main python-all-dev armhf 2.7.9-1 [1024 B]
Get:63 http://172.17.0.1/private/ stretch-staging/main python-pkg-resources all 18.4-2 [99.4 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main python-nose all 1.3.6-1 [132 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main python-setuptools all 18.4-2 [201 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main python3.5 armhf 3.5.0-3+rpi1+b1 [189 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main python3-all armhf 3.4.3-7 [942 B]
Get:68 http://172.17.0.1/private/ stretch-staging/main python3.4-dev armhf 3.4.3-10+b1 [418 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main python3-dev armhf 3.4.3-7 [1152 B]
Get:70 http://172.17.0.1/private/ stretch-staging/main python3.5-dev armhf 3.5.0-3+rpi1+b1 [419 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main python3-all-dev armhf 3.4.3-7 [972 B]
Get:72 http://172.17.0.1/private/ stretch-staging/main python3-pkg-resources all 18.4-2 [70.1 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main python3-nose all 1.3.6-1 [132 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main python3-setuptools all 18.4-2 [119 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main samtools armhf 1.2-3 [331 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-4.9_4.9.3-5 g++-5_5.2.1-23+rpi1 gcc-4.9_4.9.3-5 gcc-5_5.2.1-23+rpi1 libc6-dev_2.19-22 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-4.9_4.9.3-5 cpp-5_5.2.1-23+rpi1 cython_0.23.2+git16-ga8fbae1-1 cython3_0.23.2+git16-ga8fbae1-1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-python_2.20151103 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.2.1-4+rpi2 g++-4.9_4.9.3-5 g++-5_5.2.1-23+rpi1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9_4.9.3-5 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1 gcc-5-base_5.2.1-23+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.21-2 groff-base_1.22.3-3 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libasan1_4.9.3-5 libasan2_5.2.1-23+rpi1 libatomic1_5.2.1-23+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1 libcloog-isl4_0.18.3-1 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.2-1 libdebconfclient0_0.195 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libexpat1_2.1.0-7 libexpat1-dev_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7 libgcc-4.9-dev_4.9.3-5 libgcc-5-dev_5.2.1-23+rpi1 libgcc1_1:5.2.1-23+rpi1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-1 libgmp10_2:6.0.0+dfsg-7+rpi1 libgomp1_5.2.1-23+rpi1 libgpg-error0_1.20-1 libhts-dev_1.2.1-1+rpi1 libhts1_1.2.1-1+rpi1 libicu55_55.1-6 libisl13_0.14-2 libklibc_2.0.4-2+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpdec2_2.4.1-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libpng12-0_1.2.50-2+b2 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libpython-all-dev_2.7.9-1 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.10-5+b1 libpython2.7-dev_2.7.10-5+b1 libpython2.7-minimal_2.7.10-5+b1 libpython2.7-stdlib_2.7.10-5+b1 libpython3-all-dev_3.4.3-7 libpython3-dev_3.4.3-7 libpython3-stdlib_3.4.3-7 libpython3.4_3.4.3-10+b1 libpython3.4-dev_3.4.3-10+b1 libpython3.4-minimal_3.4.3-10+b1 libpython3.4-stdlib_3.4.3-10+b1 libpython3.5_3.5.0-3+rpi1+b1 libpython3.5-dev_3.5.0-3+rpi1+b1 libpython3.5-minimal_3.5.0-3+rpi1+b1 libpython3.5-stdlib_3.5.0-3+rpi1+b1 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-1 libsqlite3-0_3.9.2-1 libss2_1.42.13-1 libssl1.0.2_1.0.2d-3 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1 libstdc++6_5.2.1-23+rpi1 libsystemd0_227-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libubsan0_5.2.1-23+rpi1 libudev1_227-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 python_2.7.9-1 python-all_2.7.9-1 python-all-dev_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python-nose_1.3.6-1 python-pkg-resources_18.4-2 python-setuptools_18.4-2 python2.7_2.7.10-5+b1 python2.7-dev_2.7.10-5+b1 python2.7-minimal_2.7.10-5+b1 python3_3.4.3-7 python3-all_3.4.3-7 python3-all-dev_3.4.3-7 python3-dev_3.4.3-7 python3-minimal_3.4.3-7 python3-nose_1.3.6-1 python3-pkg-resources_18.4-2 python3-setuptools_18.4-2 python3.4_3.4.3-10+b1 python3.4-dev_3.4.3-10+b1 python3.4-minimal_3.4.3-10+b1 python3.5_3.5.0-3+rpi1+b1 python3.5-dev_3.5.0-3+rpi1+b1 python3.5-minimal_3.5.0-3+rpi1+b1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_1.2-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_227-2 systemd-sysv_227-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 udev_227-2 util-linux_2.27.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Nov 14 07:34:14 2015 UTC using RSA key ID AFE826FB
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./python-pysam_0.8.4+ds-1.dsc
dpkg-source: info: extracting python-pysam in python-pysam-0.8.4+ds
dpkg-source: info: unpacking python-pysam_0.8.4+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.8.4+ds-1.debian.tar.xz
dpkg-source: info: applying change-htslib-statement-to-link-to-debian
dpkg-source: info: applying adding-include-hts-dirs
dpkg-source: info: applying ignore-htslib-dir.patch
dpkg-source: info: applying disable-tests-requiring-network.patch

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-c77d0fb5-cd60-4e28-8d74-c6e26715144c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package python-pysam
dpkg-buildpackage: source version 0.8.4+ds-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build python-pysam-0.8.4+ds
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
/usr/bin/make -C tests/pysam_data clean
make[1]: Entering directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* \
	*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam
make[1]: Leaving directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c
LC_ALL=C.UTF-8 dh clean --with python2,python3 --buildsystem=pybuild
   dh_testdir -O--buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py clean 
running clean
removing '/«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:184: python3.5 setup.py clean 
running clean
removing '/«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.5' does not exist -- can't clean it
I: pybuild base:184: python3.4 setup.py clean 
running clean
removing '/«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build' (and everything under it)
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-3.4' does not exist -- can't clean it
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
LC_ALL=C.UTF-8 dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_testdir -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
running config
I: pybuild base:184: python3.5 setup.py config 
running config
I: pybuild base:184: python3.4 setup.py config 
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build 
running build
running build_py
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/csamtools.pyx to pysam/csamtools.c
building 'pysam.csamtools' extension
creating build
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/pysam
creating build/temp.linux-armv7l-2.7/samtools
creating build/temp.linux-armv7l-2.7/samtools/misc
creating build/temp.linux-armv7l-2.7/samtools/test
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-armv7l-2.7/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armv7l-2.7/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamtools.o build/temp.linux-armv7l-2.7/pysam/pysam_util.o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-2.7/samtools/test/test.c.pysam.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamtools.so
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/chtslib.c -o build/temp.linux-armv7l-2.7/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/chtslib.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/csamfile.c -o build/temp.linux-armv7l-2.7/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/calignmentfile.c -o build/temp.linux-armv7l-2.7/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignmentfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so
cythoning pysam/calignedsegment.pyx to pysam/calignedsegment.c
building 'pysam.calignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/calignedsegment.c -o build/temp.linux-armv7l-2.7/pysam/calignedsegment.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignedsegment.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignedsegment.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.so
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-armv7l-2.7/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabix.o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python2.7 -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
warning: pysam/cvcf.pyx:1069:27: Unreachable code
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-armv7l-2.7/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
warning: pysam/cbcf.pyx:2464:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2464:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python2.7 -c pysam/cbcf.c -o build/temp.linux-armv7l-2.7/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/cfaidx.c -o build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/cutils.c -o build/temp.linux-armv7l-2.7/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cutils.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so
I: pybuild base:184: /usr/bin/python3.5 setup.py build 
running build
running build_py
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
copying pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
Fixing /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
cythoning pysam/csamtools.pyx to pysam/csamtools.c
building 'pysam.csamtools' extension
creating build/temp.linux-armv7l-3.5
creating build/temp.linux-armv7l-3.5/pysam
creating build/temp.linux-armv7l-3.5/samtools
creating build/temp.linux-armv7l-3.5/samtools/misc
creating build/temp.linux-armv7l-3.5/samtools/test
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/csamtools.c -o build/temp.linux-armv7l-3.5/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.5/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamtools.o build/temp.linux-armv7l-3.5/pysam/pysam_util.o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.5/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-3.5/samtools/test/test.c.pysam.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamtools.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.5/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/chtslib.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.5/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.5/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignmentfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
building 'pysam.calignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/calignedsegment.c -o build/temp.linux-armv7l-3.5/pysam/calignedsegment.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignedsegment.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignedsegment.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.5/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabix.o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python3.5m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.5m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.5/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.5m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.5/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cbcf.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/cutils.c -o build/temp.linux-armv7l-3.5/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cutils.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so
warning: pysam/cvcf.pyx:1069:27: Unreachable code
warning: pysam/cbcf.pyx:2464:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2464:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
I: pybuild base:184: /usr/bin/python3 setup.py build 
running build
running build_py
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include
copying pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
copying pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
copying samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32
Fixing /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/Pileup.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/__init__.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/namedtuple.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/version.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/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-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/Pileup.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/__init__.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/namedtuple.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/version.py /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
cythoning pysam/csamtools.pyx to pysam/csamtools.c
building 'pysam.csamtools' extension
creating build/temp.linux-armv7l-3.4
creating build/temp.linux-armv7l-3.4/pysam
creating build/temp.linux-armv7l-3.4/samtools
creating build/temp.linux-armv7l-3.4/samtools/misc
creating build/temp.linux-armv7l-3.4/samtools/test
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/csamtools.c -o build/temp.linux-armv7l-3.4/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.4/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/csamtools.o build/temp.linux-armv7l-3.4/pysam/pysam_util.o build/temp.linux-armv7l-3.4/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.4/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.4/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.4/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.4/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.4/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.4/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.4/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.4/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.4/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-3.4/samtools/test/test.c.pysam.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamtools.cpython-34m.so
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.4/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/chtslib.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/libchtslib.cpython-34m.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.4/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.4/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/csamfile.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o build/temp.linux-armv7l-3.4/pysam/samfile_util.o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamfile.cpython-34m.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.4/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.4/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/calignmentfile.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o build/temp.linux-armv7l-3.4/pysam/samfile_util.o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignmentfile.cpython-34m.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
building 'pysam.calignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/calignedsegment.c -o build/temp.linux-armv7l-3.4/pysam/calignedsegment.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignedsegment.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.4/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/calignedsegment.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o build/temp.linux-armv7l-3.4/pysam/samfile_util.o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignedsegment.cpython-34m.so
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.4/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.4/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/ctabix.o build/temp.linux-armv7l-3.4/pysam/tabix_util.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabix.cpython-34m.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python3.4m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.4/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabixproxies.cpython-34m.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.4m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.4/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cvcf.cpython-34m.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.4m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.4/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cbcf.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cbcf.cpython-34m.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.4/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cfaidx.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cfaidx.cpython-34m.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/cutils.c -o build/temp.linux-armv7l-3.4/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cutils.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cutils.cpython-34m.so
warning: pysam/cvcf.pyx:1069:27: Unreachable code
warning: pysam/cbcf.pyx:2464:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2464:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
   debian/rules override_dh_auto_test
make[1]: Entering directory '/«BUILDDIR»/python-pysam-0.8.4+ds'
cd tests && make -C pysam_data
make[2]: Entering directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS example_btag.sam > example_btag.bam
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 softclip.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index ex4.bam
samtools index rg_with_tab.bam
samtools index ex9_nofail.bam
samtools index example_btag.bam
samtools index 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
samtools index ex2_truncated.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
make[2]: Leaving directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
# dh_auto_test	# unfortunately this does not work out of the box
# see https://lists.debian.org/debian-python/2015/07/msg00064.html
# thus trying manually with unusual tricks
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd tests && if [ {version} = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi" dh_auto_test || \
	echo "Ignoring test failures"
I: pybuild base:184: cd tests && if [ 2.7 = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi
....................................................................................Segmentation fault
E: pybuild pybuild:274: test: plugin custom failed with: exit code=139: cd tests && if [ 2.7 = 2.7 ] ; then nosetests -s ; else nosetests3 -s -v ; fi
dh_auto_test: pybuild --test -i python{version} -p 2.7 --dir . returned exit code 13
Ignoring test failures
make[1]: Leaving directory '/«BUILDDIR»/python-pysam-0.8.4+ds'
 fakeroot debian/rules binary-arch
LC_ALL=C.UTF-8 dh binary-arch --with python2,python3 --buildsystem=pybuild
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
   dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py install --root /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam 
running install
running build
running build_py
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
running build_ext
skipping 'pysam/csamtools.c' Cython extension (up-to-date)
building 'pysam.csamtools' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-armv7l-2.7/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armv7l-2.7/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python2.7 -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-2.7/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamtools.o build/temp.linux-armv7l-2.7/pysam/pysam_util.o build/temp.linux-armv7l-2.7/samtools/bam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-2.7/samtools/errmod.c.pysam.o build/temp.linux-armv7l-2.7/samtools/faidx.c.pysam.o build/temp.linux-armv7l-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-2.7/samtools/padding.c.pysam.o build/temp.linux-armv7l-2.7/samtools/phase.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-2.7/samtools/sample.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats.c.pysam.o build/temp.linux-armv7l-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-2.7/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-2.7/samtools/test/test.c.pysam.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamtools.so
skipping 'pysam/chtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/chtslib.c -o build/temp.linux-armv7l-2.7/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/chtslib.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so
skipping 'pysam/csamfile.c' Cython extension (up-to-date)
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/csamfile.c -o build/temp.linux-armv7l-2.7/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/csamfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so
skipping 'pysam/calignmentfile.c' Cython extension (up-to-date)
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/calignmentfile.c -o build/temp.linux-armv7l-2.7/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armv7l-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armv7l-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/calignmentfile.o build/temp.linux-armv7l-2.7/pysam/htslib_util.o build/temp.linux-armv7l-2.7/pysam/samfile_util.o build/temp.linux-armv7l-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/ctabix.c' Cython extension (up-to-date)
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-armv7l-2.7/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabix.o build/temp.linux-armv7l-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so
skipping 'pysam/ctabixproxies.c' Cython extension (up-to-date)
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python2.7 -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so
skipping 'pysam/cvcf.c' Cython extension (up-to-date)
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-armv7l-2.7/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so
skipping 'pysam/cbcf.c' Cython extension (up-to-date)
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python2.7 -c pysam/cbcf.c -o build/temp.linux-armv7l-2.7/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so
skipping 'pysam/cfaidx.c' Cython extension (up-to-date)
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/cfaidx.c -o build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so
skipping 'pysam/cutils.c' Cython extension (up-to-date)
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python2.7 -c pysam/cutils.c -o build/temp.linux-armv7l-2.7/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-2.7/pysam/cutils.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so
running install_lib
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignedsegment.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/__init__.pyc -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/Pileup.pyc -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/version.pyc -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamtools.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/csamfile.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/calignmentfile.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabix.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/ctabixproxies.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cvcf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cbcf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cfaidx.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_2.7/build/pysam/cutils.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/namedtuple.py to namedtuple.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc
running install_egg_info
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:184: /usr/bin/python3.5 setup.py install --root /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam 
running install
running build
running build_py
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
running build_ext
cythoning pysam/csamtools.pyx to pysam/csamtools.c
building 'pysam.csamtools' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/csamtools.c -o build/temp.linux-armv7l-3.5/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.5/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.5m -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-3.5/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamtools.o build/temp.linux-armv7l-3.5/pysam/pysam_util.o build/temp.linux-armv7l-3.5/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.5/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.5/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.5/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.5/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.5/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.5/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-3.5/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-3.5/samtools/test/test.c.pysam.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamtools.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.5/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/chtslib.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.5/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/csamfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.5/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.5/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.5/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/calignmentfile.o build/temp.linux-armv7l-3.5/pysam/htslib_util.o build/temp.linux-armv7l-3.5/pysam/samfile_util.o build/temp.linux-armv7l-3.5/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.5/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabix.o build/temp.linux-armv7l-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python3.5m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.5m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.5/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.5m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.5/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cbcf.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cfaidx.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.5m -c pysam/cutils.c -o build/temp.linux-armv7l-3.5/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.5/pysam/cutils.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so
running install_lib
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignedsegment.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamtools.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/csamfile.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/calignmentfile.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabix.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/ctabixproxies.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cvcf.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cbcf.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cfaidx.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.5/build/pysam/cutils.cpython-35m-arm-linux-gnueabihf.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/Pileup.py to Pileup.cpython-35.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/__init__.py to __init__.cpython-35.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/namedtuple.py to namedtuple.cpython-35.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/version.py to version.cpython-35.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam/include/__init__.py to __init__.cpython-35.pyc
running install_egg_info
running egg_info
writing top-level names to pysam.egg-info/top_level.txt
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: pysam/cvcf.pyx:1069:27: Unreachable code
warning: pysam/cbcf.pyx:2464:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2464:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.5/dist-packages/pysam-0.8.4.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:184: /usr/bin/python3 setup.py install --root /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam 
running install
running build
running build_py
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
running build_ext
cythoning pysam/csamtools.pyx to pysam/csamtools.c
building 'pysam.csamtools' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/csamtools.c -o build/temp.linux-armv7l-3.4/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/pysam_util.c -o build/temp.linux-armv7l-3.4/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/pysam_util.c:4:0:
samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 static inline int bam_is_big_endian()
                   ^
pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 const char *samtools_version()
             ^
pysam/pysam_util.c: In function ‘samtools_version’:
pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’:
samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable]
     bam_header_t *old;
                   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/errmod.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/faidx.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’:
samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/padding.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/phase.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/sample.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/stats.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/misc/md5.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include -I/usr/include/python3.4m -c samtools/test/test.c.pysam.c -o build/temp.linux-armv7l-3.4/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/csamtools.o build/temp.linux-armv7l-3.4/pysam/pysam_util.o build/temp.linux-armv7l-3.4/samtools/bam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2bcf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam2depth.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_aux.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_cat.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_color.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_flags.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_import.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_index.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_lpileup.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_mate.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_md.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_plbuf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_plcmd.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_reheader.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_rmdup.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_sort.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_split.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_stat.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bam_tview_html.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bamshuf.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bedcov.c.pysam.o build/temp.linux-armv7l-3.4/samtools/bedidx.c.pysam.o build/temp.linux-armv7l-3.4/samtools/cut_target.c.pysam.o build/temp.linux-armv7l-3.4/samtools/errmod.c.pysam.o build/temp.linux-armv7l-3.4/samtools/faidx.c.pysam.o build/temp.linux-armv7l-3.4/samtools/kprobaln.c.pysam.o build/temp.linux-armv7l-3.4/samtools/padding.c.pysam.o build/temp.linux-armv7l-3.4/samtools/phase.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam_header.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sam_view.c.pysam.o build/temp.linux-armv7l-3.4/samtools/sample.c.pysam.o build/temp.linux-armv7l-3.4/samtools/stats.c.pysam.o build/temp.linux-armv7l-3.4/samtools/stats_isize.c.pysam.o build/temp.linux-armv7l-3.4/samtools/misc/ace2sam.c.pysam.o build/temp.linux-armv7l-3.4/samtools/misc/md5.c.pysam.o build/temp.linux-armv7l-3.4/samtools/test/test.c.pysam.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamtools.cpython-34m.so
cythoning pysam/chtslib.pyx to pysam/chtslib.c
building 'pysam.libchtslib' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/chtslib.c -o build/temp.linux-armv7l-3.4/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/chtslib.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/chtslib.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/libchtslib.cpython-34m.so
cythoning pysam/csamfile.pyx to pysam/csamfile.c
building 'pysam.csamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/csamfile.c -o build/temp.linux-armv7l-3.4/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/csamfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.4/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/csamfile.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o build/temp.linux-armv7l-3.4/pysam/samfile_util.o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamfile.cpython-34m.so
cythoning pysam/calignmentfile.pyx to pysam/calignmentfile.c
building 'pysam.calignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/calignmentfile.c -o build/temp.linux-armv7l-3.4/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/calignmentfile.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’:
pysam/calignmentfile.c:22807:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/htslib_util.c -o build/temp.linux-armv7l-3.4/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/htslib_util.c:9:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/htslib_util.c:25:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity()
     ^
pysam/htslib_util.c:31:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_hts_verbose();
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c pysam/samfile_util.c -o build/temp.linux-armv7l-3.4/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.4m -c samtools/kprobaln.c -o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
samtools/kprobaln.c: In function ‘kpa_glocal’:
samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/calignmentfile.o build/temp.linux-armv7l-3.4/pysam/htslib_util.o build/temp.linux-armv7l-3.4/pysam/samfile_util.o build/temp.linux-armv7l-3.4/samtools/kprobaln.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignmentfile.cpython-34m.so
skipping 'pysam/calignedsegment.c' Cython extension (up-to-date)
cythoning pysam/ctabix.pyx to pysam/ctabix.c
building 'pysam.ctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/ctabix.c -o build/temp.linux-armv7l-3.4/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/ctabix.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’:
pysam/ctabix.c:5821:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                     ^
pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’:
pysam/ctabix.c:10344:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum));
             ^
pysam/ctabix.c: At top level:
pysam/ctabix.c:10311:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function]
 static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/tabix_util.c -o build/temp.linux-armv7l-3.4/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/ctabix.o build/temp.linux-armv7l-3.4/pysam/tabix_util.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabix.cpython-34m.so
cythoning pysam/ctabixproxies.pyx to pysam/ctabixproxies.c
building 'pysam.ctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/usr/include/python3.4m -c pysam/ctabixproxies.c -o build/temp.linux-armv7l-3.4/pysam/ctabixproxies.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/ctabixproxies.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabixproxies.cpython-34m.so
cythoning pysam/cvcf.pyx to pysam/cvcf.c
building 'pysam.cvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.4m -c pysam/cvcf.c -o build/temp.linux-armv7l-3.4/pysam/cvcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cvcf.c:248:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’:
pysam/cvcf.c:21558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                ^
pysam/cvcf.c:16978:10: note: ‘__pyx_v_qual’ was declared here
   double __pyx_v_qual;
          ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cvcf.o -lz -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cvcf.cpython-34m.so
cythoning pysam/cbcf.pyx to pysam/cbcf.c
building 'pysam.cbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ihtslib -I/usr/include -I/usr/include/python3.4m -c pysam/cbcf.c -o build/temp.linux-armv7l-3.4/pysam/cbcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cbcf.c:246:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
pysam/cbcf.c: In function ‘__pyx_gb_5pysam_4cbcf_19char_array_to_tuple_2generator29’:
pysam/cbcf.c:3644:55: warning: passing argument 1 of ‘__pyx_f_5pysam_6cutils_charptr_to_str’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
     __pyx_t_3 = __pyx_f_5pysam_6cutils_charptr_to_str((__pyx_cur_scope->__pyx_outer_scope->__pyx_v_a[__pyx_cur_scope->__pyx_v_i]), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                       ^
pysam/cbcf.c:3644:55: note: expected ‘char *’ but argument is of type ‘const char *’
pysam/cbcf.c: In function ‘__pyx_pf_5pysam_4cbcf_19VariantHeaderRecord_2__bool__’:
pysam/cbcf.c:5599:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
     return (PyObject *) gen;
            ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cbcf.o -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cbcf.cpython-34m.so
cythoning pysam/cfaidx.pyx to pysam/cfaidx.c
building 'pysam.cfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/cfaidx.c -o build/temp.linux-armv7l-3.4/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
In file included from pysam/cfaidx.c:247:0:
pysam/htslib_util.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int hts_get_verbosity();
 ^
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cfaidx.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cfaidx.cpython-34m.so
cythoning pysam/cutils.pyx to pysam/cutils.c
building 'pysam.cutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -I/usr/include -I/usr/include/python3.4m -c pysam/cutils.c -o build/temp.linux-armv7l-3.4/pysam/cutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.4/pysam/cutils.o -Lpysam -lz -lhts -o /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cutils.cpython-34m.so
running install_lib
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/Pileup.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/namedtuple.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/version.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/__init__.py -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam2bcf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam_endian.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam_lpileup.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam_plbuf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/bam_tview.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/errmod.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/kprobaln.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/pysam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/sam.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/sam_header.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/sample.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/samtools.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/stats_isize.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/version.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools
creating /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32/xcurses.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32/zconf.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/include/samtools/win32/zlib.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/samtools/win32
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignedsegment.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignmentfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cbcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cfaidx.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/chtslib.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamfile.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamtools.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabix.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabixproxies.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cutils.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cvcf.pxd -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/htslib_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/pysam_stream.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/pysam_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/samfile_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/tabix_util.h -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam
renaming extension calignedsegment.cpython-34m.so -> calignedsegment.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignedsegment.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/calignedsegment.cpython-34m-arm-linux-gnueabihf.so
renaming extension csamtools.cpython-34m.so -> csamtools.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamtools.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/csamtools.cpython-34m-arm-linux-gnueabihf.so
renaming extension libchtslib.cpython-34m.so -> libchtslib.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/libchtslib.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/libchtslib.cpython-34m-arm-linux-gnueabihf.so
renaming extension csamfile.cpython-34m.so -> csamfile.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/csamfile.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/csamfile.cpython-34m-arm-linux-gnueabihf.so
renaming extension calignmentfile.cpython-34m.so -> calignmentfile.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/calignmentfile.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/calignmentfile.cpython-34m-arm-linux-gnueabihf.so
renaming extension ctabix.cpython-34m.so -> ctabix.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabix.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/ctabix.cpython-34m-arm-linux-gnueabihf.so
renaming extension ctabixproxies.cpython-34m.so -> ctabixproxies.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/ctabixproxies.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/ctabixproxies.cpython-34m-arm-linux-gnueabihf.so
renaming extension cvcf.cpython-34m.so -> cvcf.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cvcf.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/cvcf.cpython-34m-arm-linux-gnueabihf.so
renaming extension cbcf.cpython-34m.so -> cbcf.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cbcf.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/cbcf.cpython-34m-arm-linux-gnueabihf.so
renaming extension cfaidx.cpython-34m.so -> cfaidx.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cfaidx.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/cfaidx.cpython-34m-arm-linux-gnueabihf.so
renaming extension cutils.cpython-34m.so -> cutils.cpython-34m-arm-linux-gnueabihf.so
copying /«BUILDDIR»/python-pysam-0.8.4+ds/.pybuild/pythonX.Y_3.4/build/pysam/cutils.cpython-34m.so -> /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/cutils.cpython-34m-arm-linux-gnueabihf.so
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/Pileup.py to Pileup.cpython-34.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/__init__.py to __init__.cpython-34.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/namedtuple.py to namedtuple.cpython-34.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/version.py to version.cpython-34.pyc
byte-compiling /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam/include/__init__.py to __init__.cpython-34.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: pysam/cvcf.pyx:1069:27: Unreachable code
warning: pysam/cbcf.pyx:2464:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2464:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: pysam/cbcf.pyx:2505:30: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'tests/pysam_data'
warning: no files found matching 'tests/tabix_data'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /«BUILDDIR»/python-pysam-0.8.4+ds/debian/python3-pysam/usr/lib/python3.4/dist-packages/pysam-0.8.4.egg-info
Skipping SOURCES.txt
running install_scripts
   debian/rules override_dh_install
make[1]: Entering directory '/«BUILDDIR»/python-pysam-0.8.4+ds'
/usr/bin/make -C tests/pysam_data clean
make[2]: Entering directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* \
	*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam
make[2]: Leaving directory '/«BUILDDIR»/python-pysam-0.8.4+ds/tests/pysam_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c
dh_install -Xtest.gtf.gz
make[1]: Leaving directory '/«BUILDDIR»/python-pysam-0.8.4+ds'
   dh_installdocs -a -O--buildsystem=pybuild
   dh_installchangelogs -a -O--buildsystem=pybuild
   dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:328: renaming calignedsegment.so to calignedsegment.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming calignmentfile.so to calignmentfile.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cbcf.so to cbcf.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cfaidx.so to cfaidx.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming csamfile.so to csamfile.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming csamtools.so to csamtools.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming ctabix.so to ctabix.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming ctabixproxies.so to ctabixproxies.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cutils.so to cutils.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming cvcf.so to cvcf.arm-linux-gnueabihf.so
I: dh_python2 fs:328: renaming libchtslib.so to libchtslib.arm-linux-gnueabihf.so
   dh_python3 -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
   dh_fixperms -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -a -O--buildsystem=pybuild
   dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Provides}
dpkg-gencontrol: warning: package python-pysam: unused substitution variable ${python:Versions}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Provides}
dpkg-gencontrol: warning: package python3-pysam: unused substitution variable ${python3:Versions}
   dh_md5sums -a -O--buildsystem=pybuild
   dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.8.4+ds-1_armhf.deb'.
dpkg-deb: building package 'python-pysam' in '../python-pysam_0.8.4+ds-1_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../python-pysam_0.8.4+ds-1_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build python-pysam-0.8.4+ds
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151119-0736

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


python-pysam_0.8.4+ds-1_armhf.changes:
──────────────────────────────────────

Format: 1.8
Date: Fri, 13 Nov 2015 22:15:14 -0800
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: armhf
Version: 0.8.4+ds-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@ghraoui.name>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format (
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Changes:
 python-pysam (0.8.4+ds-1) unstable; urgency=medium
 .
   * Add version constraints to build-dependencies.
   * Drop ds suffix versioning.
   * Imported Upstream version 0.8.4+ds
   * Remove patches applied upstream
   * Refresh existing patches
   * Refine d/rules
   * Set Vcs-Browser to point to cgit rather than gitweb
   * Reduce dependencies in autopktest dependencies
   * Replace patch for network-dependent tests
   * Add new lintian overrides
Checksums-Sha1:
 edd7daf7a267f526b95f96abc7bfa195b8cc13d3 716190 python-pysam_0.8.4+ds-1_armhf.deb
 6d9c46cac59de8c0863e3f97d197ac00f85b4780 1019368 python3-pysam_0.8.4+ds-1_armhf.deb
Checksums-Sha256:
 870eb3308deee6db3038bb5e0c85868d45e283b013b54a6c56fd3f1ab249f467 716190 python-pysam_0.8.4+ds-1_armhf.deb
 8bb95becece88be97d68d02385adb07210f06ad94bc1faa025a2bc127fdbe434 1019368 python3-pysam_0.8.4+ds-1_armhf.deb
Files:
 843e3896f99689415c7ebd908378b9e1 716190 python optional python-pysam_0.8.4+ds-1_armhf.deb
 0d16e6b33bb28135d70a8051f95e8b41 1019368 python optional python3-pysam_0.8.4+ds-1_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


python-pysam_0.8.4+ds-1_armhf.deb
─────────────────────────────────

 new debian package, version 2.0.
 size 716190 bytes: control archive=2550 bytes.
     683 bytes,    15 lines      control              
    5382 bytes,    57 lines      md5sums              
     160 bytes,     9 lines   *  postinst             #!/bin/sh
     259 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-pysam
 Version: 0.8.4+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2808
 Depends: libc6 (>= 2.7), libhts1 (>= 1.2.1), zlib1g (>= 1:1.2.3.3), python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~)
 Section: python
 Priority: optional
 Homepage: https://github.com/pysam-developers/pysam
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 2.

drwxr-xr-x root/root         0 2015-11-19 07:35 ./
drwxr-xr-x root/root         0 2015-11-19 07:35 ./usr/
drwxr-xr-x root/root         0 2015-11-19 07:06 ./usr/lib/
drwxr-xr-x root/root         0 2015-11-19 07:06 ./usr/lib/python2.7/
drwxr-xr-x root/root         0 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root         0 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info/
-rw-r--r-- root/root      1009 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info/dependency_links.txt
-rw-r--r-- root/root         1 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info/not-zip-safe
-rw-r--r-- root/root         6 2015-11-19 07:06 ./usr/lib/python2.7/dist-packages/pysam-0.8.4.egg-info/top_level.txt
drwxr-xr-x root/root         0 2015-11-19 07:35 ./usr/lib/python2.7/dist-packages/pysam/
-rw-r--r-- root/root      8305 2015-11-09 22:42 ./usr/lib/python2.7/dist-packages/pysam/Pileup.py
-rw-r--r-- root/root      6266 2015-11-09 22:42 ./usr/lib/python2.7/dist-packages/pysam/__init__.py
-rw-r--r-- root/root    311492 2015-11-19 07:35 ./usr/lib/python2.7/dist-packages/pysam/calignedsegment.arm-linux-gnueabihf.so
-rw-r--r-- root/root      3041 2015-11-09 22:42 ./usr/lib/python2.7/dist-packages/pysam/calignedsegment.pxd
-rw-r--r-- root/root    332692 2015-11-19 07:35 ./usr/lib/python2.7/dist-packages/pysam/calignmentfile.arm-linux-gnueabihf.so
-rw-r--r-- root/root      3986 2015-11-09 22:42 ./usr/lib/python2.7/dist-packages/pysam/calignmentfile.pxd
-rw-r--r-- root/root    433384 2015-11-19 07:35 ./usr/lib/python2.7/dist-packages/pysam/cbcf.arm-linux-gnueabihf.so
-rw-r--r-- root/root      4873 2015-11-09 22:42 ./usr/lib/python2.7/dist-packages/pysam/cbcf.pxd
-rw-r--r-- root/root    119512 2015-11-19 07:35 ./usr/lib/python2.7/dist-packages/pysam/cfaidx.arm-linux-gnueabihf.so
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drwxr-xr-x root/root         0 2015-11-19 07:35 ./usr/share/doc/
drwxr-xr-x root/root         0 2015-11-19 07:35 ./usr/share/doc/python-pysam/
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-rw-r--r-- root/root      6685 2015-10-06 07:21 ./usr/share/doc/python-pysam/copyright
drwxr-xr-x root/root         0 2015-11-19 07:35 ./usr/share/lintian/
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python3-pysam_0.8.4+ds-1_armhf.deb
──────────────────────────────────

 new debian package, version 2.0.
 size 1019368 bytes: control archive=2932 bytes.
     681 bytes,    16 lines      control              
    6670 bytes,    68 lines      md5sums              
     170 bytes,     9 lines   *  postinst             #!/bin/sh
     399 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-pysam
 Source: python-pysam
 Version: 0.8.4+ds-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5249
 Depends: libc6 (>= 2.7), libhts1 (>= 1.2.1), zlib1g (>= 1:1.2.3.3), python3 (<< 3.6), python3 (>= 3.4~)
 Section: python
 Priority: optional
 Homepage: https://github.com/pysam-developers/pysam
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 3.

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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 104756
Build-Time: 5322
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 590
Job: python-pysam_0.8.4+ds-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 5978
Source-Version: 0.8.4+ds-1
Space: 104756
Status: successful
Version: 0.8.4+ds-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20151119-0736
Build needed 01:39:38, 104756k disc space