Raspbian Package Auto-Building

Build log for python-pysam (0.10.0+ds-1) on armhf

python-pysam0.10.0+ds-1armhf → 2017-04-10 04:39:40

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01

+==============================================================================+
| python-pysam 0.10.0+ds-1 (armhf)             Mon, 10 Apr 2017 03:41:22 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.10.0+ds-1
Source Version: 0.10.0+ds-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-620828c5-8881-4ae9-a59f-891b3fe6cea7' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9732 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 23s (905 kB/s)
Reading package lists...

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/python-pysam.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2315 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main python-pysam 0.10.0+ds-1 (dsc) [2447 B]
Get:2 http://172.17.0.1/private stretch-staging/main python-pysam 0.10.0+ds-1 (tar) [2304 kB]
Get:3 http://172.17.0.1/private stretch-staging/main python-pysam 0.10.0+ds-1 (diff) [7944 B]
Fetched 2315 kB in 0s (9475 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-TcgA2P/python-pysam-0.10.0+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-TcgA2P' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-aF8GwV/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-aF8GwV/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-aF8GwV/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3019 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-aF8GwV/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13028 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose
Filtered Build-Depends: debhelper (>= 9), dh-python, libhts-dev (>= 1.3.2), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.3.1), bcftools (>= 1.3.1), python-nose, python3-nose
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-aF8GwV/apt_archive/sbuild-build-depends-python-pysam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-python-pysam-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Sources [577 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Packages [660 B]
Fetched 2570 B in 0s (3711 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-aF8GwV/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
  libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev libffi6
  libfile-stripnondeterminism-perl libglib2.0-0 libgnutls30 libgsl2
  libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu57 libidn2-0
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14
  libp11-kit0 libpipeline1 libpsl5 libpython-all-dev libpython-dev
  libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
  libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib
  librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1
  libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-all python-all-dev python-dev
  python-minimal python-nose python-pkg-resources python-setuptools python2.7
  python2.7-dev python2.7-minimal python3 python3-all python3-all-dev
  python3-dev python3-minimal python3-nose python3-pkg-resources
  python3-setuptools python3.5 python3.5-dev python3.5-minimal samtools tabix
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc python-numpy python-matplotlib
  texlive-latex-recommended wamerican | wordlist whois vacation cython-doc
  dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin
  gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser
  libmail-box-perl python-doc python-tk python-coverage python-nose-doc
  python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk
  python3-venv python3.5-venv python3.5-doc
Recommended packages:
  curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev
  xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism file
  gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
  libcroco3 libcurl3-gnutls libexpat1 libexpat1-dev libffi6
  libfile-stripnondeterminism-perl libglib2.0-0 libgnutls30 libgsl2
  libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu57 libidn2-0
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
  libldap-common libmagic-mgc libmagic1 libmpdec2 libnettle6 libnghttp2-14
  libp11-kit0 libpipeline1 libpsl5 libpython-all-dev libpython-dev
  libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
  libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib
  librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1
  libtasn1-6 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
  mime-support po-debconf python python-all python-all-dev python-dev
  python-minimal python-nose python-pkg-resources python-setuptools python2.7
  python2.7-dev python2.7-minimal python3 python3-all python3-all-dev
  python3-dev python3-minimal python3-nose python3-pkg-resources
  python3-setuptools python3.5 python3.5-dev python3.5-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded.
Need to get 105 MB/106 MB of archives.
After this operation, 234 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aF8GwV/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [866 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-2 [62.2 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0e-1 [1103 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-minimal armhf 3.5.3-1 [566 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python3.5-minimal armhf 3.5.3-1 [1442 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf python3-minimal armhf 3.5.3-1 [35.3 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libmpdec2 armhf 2.4.2-1 [67.5 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-stdlib armhf 3.5.3-1 [2091 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf python3.5 armhf 3.5.3-1 [229 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libpython3-stdlib armhf 3.5.3-1 [18.6 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf dh-python all 2.20170125 [86.8 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf python3 armhf 3.5.3-1 [21.6 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-3 [221 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-3 [104 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-3 [63.2 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.10-1 [45.3 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.8-3 [822 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-3 [84.5 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-3 [194 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libgsl2 armhf 2.3+dfsg-1 [722 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libidn2-0 armhf 0.16-1 [59.3 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.18.1-1 [68.0 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libpsl5 armhf 0.17.0-3 [40.8 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.52.1-3 [258 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-2+rpi1 [215 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf bcftools armhf 1.3.1-1 [281 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf cython armhf 0.25.2~b0-2 [1698 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf cython3 armhf 0.25.2~b0-2 [1704 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.032-1 [15.8 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.032-1 [9888 B]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libexpat1-dev armhf 2.2.0-2 [116 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.2-2+rpi1 [270 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libpython2.7 armhf 2.7.13-2 [916 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-dev armhf 2.7.13-2 [27.6 MB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libpython-dev armhf 2.7.13-2 [20.0 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libpython-all-dev armhf 2.7.13-2 [958 B]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libpython3.5 armhf 3.5.3-1 [1169 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libpython3.5-dev armhf 3.5.3-1 [36.9 MB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libpython3-dev armhf 3.5.3-1 [18.7 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libpython3-all-dev armhf 3.5.3-1 [960 B]
Get:84 http://172.17.0.1/private stretch-staging/main armhf python-all armhf 2.7.13-2 [940 B]
Get:85 http://172.17.0.1/private stretch-staging/main armhf python2.7-dev armhf 2.7.13-2 [276 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf python-dev armhf 2.7.13-2 [1130 B]
Get:87 http://172.17.0.1/private stretch-staging/main armhf python-all-dev armhf 2.7.13-2 [962 B]
Get:88 http://172.17.0.1/private stretch-staging/main armhf python-pkg-resources all 33.1.1-1 [166 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf python-nose all 1.3.7-2 [132 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf python-setuptools all 33.1.1-1 [297 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf python3-all armhf 3.5.3-1 [934 B]
Get:92 http://172.17.0.1/private stretch-staging/main armhf python3.5-dev armhf 3.5.3-1 [413 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf python3-dev armhf 3.5.3-1 [1158 B]
Get:94 http://172.17.0.1/private stretch-staging/main armhf python3-all-dev armhf 3.5.3-1 [962 B]
Get:95 http://172.17.0.1/private stretch-staging/main armhf python3-pkg-resources all 33.1.1-1 [137 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf python3-nose all 1.3.7-2 [132 kB]
Get:97 http://172.17.0.1/private stretch-staging/main armhf python3-setuptools all 33.1.1-1 [215 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-3 [220 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf tabix armhf 1.3.2-2+rpi1 [204 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
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Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up libtasn1-6:armhf (4.10-1) ...
Setting up libmagic-mgc (1:5.29-3) ...
Setting up libmagic1:armhf (1:5.29-3) ...
Setting up libhogweed4:armhf (3.3-1) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-9) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libexpat1-dev:armhf (2.2.0-2) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.13-2) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up libmpdec2:armhf (2.4.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.032-1) ...
Setting up libidn2-0:armhf (0.16-1) ...
Setting up libpsl5:armhf (0.17.0-3) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up libpython3.5-stdlib:armhf (3.5.3-1) ...
Setting up python2.7 (2.7.13-2) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-3) ...
Setting up libkrb5support0:armhf (1.15-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libpython-stdlib:armhf (2.7.13-2) ...
Setting up libp11-kit0:armhf (0.23.3-2) ...
Setting up libpython2.7:armhf (2.7.13-2) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-dev:armhf (2.7.13-2) ...
Setting up python2.7-dev (2.7.13-2) ...
Setting up python (2.7.13-2) ...
Setting up libtool (2.4.6-2) ...
Setting up python3.5 (3.5.3-1) ...
Setting up libpython3-stdlib:armhf (3.5.3-1) ...
Setting up libpython-dev:armhf (2.7.13-2) ...
Setting up libk5crypto3:armhf (1.15-1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libpython3.5:armhf (3.5.3-1) ...
Setting up python-dev (2.7.13-2) ...
Setting up libgnutls30:armhf (3.5.8-3) ...
Setting up libpython-all-dev:armhf (2.7.13-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up python-pkg-resources (33.1.1-1) ...
Setting up libpython3.5-dev:armhf (3.5.3-1) ...
Setting up cython (0.25.2~b0-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-3) ...
Setting up libkrb5-3:armhf (1.15-1) ...
Setting up python3.5-dev (3.5.3-1) ...
Setting up python-nose (1.3.7-2) ...
Setting up python-all (2.7.13-2) ...
Setting up libpython3-dev:armhf (3.5.3-1) ...
Setting up python-setuptools (33.1.1-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libgssapi-krb5-2:armhf (1.15-1) ...
Setting up python-all-dev (2.7.13-2) ...
Setting up libpython3-all-dev:armhf (3.5.3-1) ...
Setting up libcurl3-gnutls:armhf (7.52.1-3) ...
Setting up tabix (1.3.2-2+rpi1) ...
Setting up libhts1:armhf (1.3.2-2+rpi1) ...
Setting up libhts-dev:armhf (1.3.2-2+rpi1) ...
Setting up samtools (1.3.1-3) ...
Setting up bcftools (1.3.1-1) ...
Setting up dh-autoreconf (14) ...
Setting up python3 (3.5.3-1) ...
Setting up python3-dev (3.5.3-1) ...
Setting up python3-pkg-resources (33.1.1-1) ...
Setting up dh-strip-nondeterminism (0.032-1) ...
Setting up python3-nose (1.3.7-2) ...
Setting up python3-all (3.5.3-1) ...
Setting up cython3 (0.25.2~b0-2) ...
Setting up python3-setuptools (33.1.1-1) ...
Setting up dh-python (2.20170125) ...
Setting up debhelper (10.2.5) ...
Setting up python3-all-dev (3.5.3-1) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-9) ...

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

Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-3 dpkg-dev_1.18.23 g++-6_6.3.0-11+rpi1 gcc-6_6.3.0-11+rpi1 libc6-dev_2.24-9 libstdc++-6-dev_6.3.0-11+rpi1 libstdc++6_6.3.0-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.8+rpi1 base-passwd_3.5.43 bash_4.4-4 bcftools_1.3.1-1 binutils_2.28-3 bsdmainutils_9.0.12 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-2 cpp-6_6.3.0-11+rpi1 cython_0.25.2~b0-2 cython3_0.25.2~b0-2 dash_0.5.8-2.4 debconf_1.5.60 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1 dh-autoreconf_14 dh-python_2.20170125 dh-strip-nondeterminism_0.032-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.23 dpkg-dev_1.18.23 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.29-3 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-2 g++-6_6.3.0-11+rpi1 gcc_4:6.3.0-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.3.0-11+rpi1 gcc-6-base_6.3.0-11+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gnupg-l10n_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg5.0_1.4 libarchive-zip-perl_1.59-1 libasan3_6.3.0-11+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9 libc-dev-bin_2.24-9 libc6_2.24-9 libc6-dev_2.24-9 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-11+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-3 libcurl3-gnutls_7.52.1-3 libdb5.3_5.3.28-12 libdbus-1-3_1.10.16-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.23 libdrm2_2.4.74-1 libexpat1_2.2.0-2 libexpat1-dev_2.2.0-2 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.032-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.3.0-11+rpi1 libgcc1_1:6.3.0-11+rpi1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-3 libgomp1_6.3.0-11+rpi1 libgpg-error0_1.26-2 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15-1 libhogweed4_3.3-1 libhts-dev_1.3.2-2+rpi1 libhts1_1.3.2-2+rpi1 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-5 libisl15_0.18-1 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-3 libldap-common_2.4.44+dfsg-3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-3 libmagic1_1:5.29-3 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1 libnghttp2-14_1.18.1-1 libnpth0_1.3-1 libp11-kit0_0.23.3-2 libpam-modules_1.1.8-3.5 libpam-modules-bin_1.1.8-3.5 libpam-runtime_1.1.8-3.5 libpam0g_1.1.8-3.5 libpcre3_2:8.39-3 libperl5.24_5.24.1-2 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libpsl5_0.17.0-3 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.5.3-1 libpython3-dev_3.5.3-1 libpython3-stdlib_3.5.3-1 libpython3.5_3.5.3-1 libpython3.5-dev_3.5.3-1 libpython3.5-minimal_3.5.3-1 libpython3.5-stdlib_3.5.3-1 libreadline7_7.0-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-3 libss2_1.43.4-2 libssh2-1_1.7.0-1 libssl1.1_1.1.0e-1 libstdc++-6-dev_6.3.0-11+rpi1 libstdc++6_6.3.0-11+rpi1 libsystemd0_232-22 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-11+rpi1 libudev1_232-22 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.10-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-1 multiarch-support_2.24-9 nano_2.7.4-1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4 patch_2.7.5-1 perl_5.24.1-2 perl-base_5.24.1-2 perl-modules-5.24_5.24.1-2 pinentry-curses_1.0.0-2 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-nose_1.3.7-2 python-pkg-resources_33.1.1-1 python-setuptools_33.1.1-1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1 python3-all_3.5.3-1 python3-all-dev_3.5.3-1 python3-dev_3.5.3-1 python3-minimal_3.5.3-1 python3-nose_1.3.7-2 python3-pkg-resources_33.1.1-1 python3-setuptools_33.1.1-1 python3.5_3.5.3-1 python3.5-dev_3.5.3-1 python3.5-minimal_3.5.3-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-2 samtools_1.3.1-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-22 systemd-sysv_232-22 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tabix_1.3.2-2+rpi1 tar_1.29b-1.1 tzdata_2017b-1 udev_232-22 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Jan 26 12:39:57 2017 UTC
gpgv:                using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.10.0+ds-1.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.10.0+ds
dpkg-source: info: unpacking python-pysam_0.10.0+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.10.0+ds-1.debian.tar.xz
dpkg-source: info: applying rpath.patch
dpkg-source: info: applying htslib-external-config.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-620828c5-8881-4ae9-a59f-891b3fe6cea7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.10.0+ds-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build python-pysam-0.10.0+ds
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
find . -name "tmp_*" -delete
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c
dh clean --with python2,python3 --buildsystem=pybuild
   dh_testdir -O--buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds'
dh_auto_clean
I: pybuild base:184: python2.7 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:184: python3.5 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.5' does not exist -- can't clean it
rm -f \
	pysam/config.py \
	pysam/config.h \
	samtools/config.h
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds'
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_testdir -a -O--buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:184: python3.5 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:184: /usr/bin/python setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libchtslib.so
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
building 'pysam.libcsamfile' extension
creating build/temp.linux-armhf-2.7/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcsamfile.so
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignmentfile.so
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-armhf-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o build/temp.linux-armhf-2.7/pysam/htslib_util.o build/temp.linux-armhf-2.7/pysam/samfile_util.o build/temp.linux-armhf-2.7/samtools/kprobaln.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcalignedsegment.so
cythoning pysam/libctabix.pyx to pysam/libctabix.c
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o build/temp.linux-armhf-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabix.so
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libctabixproxies.so
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.66’:
pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcvcf.so
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbcf.so
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcbgzf.so
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcfaidx.so
cythoning pysam/libcutils.pyx to pysam/libcutils.c
building 'pysam.libcutils' extension
creating build/temp.linux-armhf-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
     __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
     __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:10530:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘info_rules_init’:
bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
         while ( *ss ) ss++; ss++;
         ^~~~~
bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’
         while ( *ss ) ss++; ss++;
                             ^~
bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
         while ( *ss ) ss++; ss++; n++;
         ^~~~~
bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’
         while ( *ss ) ss++; ss++; n++;
                             ^~
bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’:
bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (j=0; j<maux->nals; j++) fprintf(pysam_stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n");
     ^~~
bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’
     for (j=0; j<maux->nals; j++) fprintf(pysam_stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n");
                                                                                                               ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-9xgeTe/python2.7-2.7.13=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/errmod.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Lpysam -L/usr/lib/arm-linux-gnueabihf -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build/pysam/libcutils.so
I: pybuild base:184: /usr/bin/python3 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/namedtuple.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/samfile_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
copying pysam/tabix_util.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/bam_tview.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/errmod.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/kprobaln.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/pysam.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/namedtuple.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.5
creating build/temp.linux-armhf-3.5/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.5/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libchtslib.o build/temp.linux-armhf-3.5/pysam/htslib_util.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libchtslib.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
creating build/temp.linux-armhf-3.5/samtools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.5/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armhf-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcsamfile.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o build/temp.linux-armhf-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcsamfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.5/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23298:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:21854:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:7271:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armhf-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcalignmentfile.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o build/temp.linux-armhf-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignmentfile.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.5/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.5/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c pysam/samfile_util.c -o build/temp.linux-armhf-3.5/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c -o build/temp.linux-armhf-3.5/samtools/kprobaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcalignedsegment.o build/temp.linux-armhf-3.5/pysam/htslib_util.o build/temp.linux-armhf-3.5/pysam/samfile_util.o build/temp.linux-armhf-3.5/samtools/kprobaln.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcalignedsegment.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libctabix.c -o build/temp.linux-armhf-3.5/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:5979:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/tabix_util.c -o build/temp.linux-armhf-3.5/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libctabix.o build/temp.linux-armhf-3.5/pysam/tabix_util.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabix.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.5/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libctabixproxies.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libctabixproxies.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.5/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.67’:
pysam/libcvcf.c:23985:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcvcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcvcf.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.5/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcbcf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbcf.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.5/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcbgzf.o -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcbgzf.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.5/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcfaidx.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcfaidx.cpython-35m-arm-linux-gnueabihf.so
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
creating build/temp.linux-armhf-3.5/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/libcutils.c -o build/temp.linux-armhf-3.5/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6730:22: warning: implicit declaration of function ‘samtools_main’ [-Wimplicit-function-declaration]
     __pyx_v_retval = samtools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
pysam/libcutils.c:6759:22: warning: implicit declaration of function ‘bcftools_main’ [-Wimplicit-function-declaration]
     __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:289:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5467:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.5/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_tview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_tview_curses.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam_tview_curses.c.pysam.c:343:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp]
 #warning "No curses library is available; tview with curses is disabled."
  ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bam_tview_html.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/errmod.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/errmod.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/kprobaln.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/kprobaln.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.5/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfmerge.c.pysam.c: In function ‘info_rules_init’:
bcftools/vcfmerge.c.pysam.c:279:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
         while ( *ss ) ss++; ss++;
         ^~~~~
bcftools/vcfmerge.c.pysam.c:279:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’
         while ( *ss ) ss++; ss++;
                             ^~
bcftools/vcfmerge.c.pysam.c:305:9: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation]
         while ( *ss ) ss++; ss++; n++;
         ^~~~~
bcftools/vcfmerge.c.pysam.c:305:29: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘while’
         while ( *ss ) ss++; ss++; n++;
                             ^~
bcftools/vcfmerge.c.pysam.c: In function ‘debug_maux’:
bcftools/vcfmerge.c.pysam.c:1663:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (j=0; j<maux->nals; j++) fprintf(pysam_stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n");
     ^~~
bcftools/vcfmerge.c.pysam.c:1663:111: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’
     for (j=0; j<maux->nals; j++) fprintf(pysam_stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(pysam_stderr,"\n");
                                                                                                               ^~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isamtools -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python3.5m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.5/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.10.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.5/pysam/libcutils.o build/temp.linux-armhf-3.5/pysam/pysam_util.o build/temp.linux-armhf-3.5/samtools/bam.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_tview.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_tview_curses.c.pysam.o build/temp.linux-armhf-3.5/samtools/bam_tview_html.c.pysam.o build/temp.linux-armhf-3.5/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.5/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.5/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.5/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.5/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.5/samtools/dict.c.pysam.o build/temp.linux-armhf-3.5/samtools/errmod.c.pysam.o build/temp.linux-armhf-3.5/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.5/samtools/kprobaln.c.pysam.o build/temp.linux-armhf-3.5/samtools/padding.c.pysam.o build/temp.linux-armhf-3.5/samtools/phase.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.5/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.5/samtools/sample.c.pysam.o build/temp.linux-armhf-3.5/samtools/stats.c.pysam.o build/temp.linux-armhf-3.5/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.5/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.5/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.5/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.5/bcftools/em.c.pysam.o build/temp.linux-armhf-3.5/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.5/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.5/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.5/bcftools/main.c.pysam.o build/temp.linux-armhf-3.5/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.5/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.5/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.5/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.5/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.5/bcftools/version.c.pysam.o -Lpysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_3.5/build/pysam/libcutils.cpython-35m-arm-linux-gnueabihf.so
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex_spliced.sam > ex_spliced.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS test_query_position.sam > test_query_position.bam
touch tmp.list
samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam
rm -f tmp.list
samtools view -bS ex6.sam > ex6.bam
samtools view -bS example_user_header.sam > example_user_header.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index ex4.bam
samtools index rg_with_tab.bam
samtools index ex_spliced.bam
samtools index ex9_nofail.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex6.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz    # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz  # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz    # create tbi index
bcftools index example_vcf40.vcf.gz  # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz    # create tbi index
bcftools index missing_genotypes.vcf.gz  # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz    # create tbi index
bcftools index example_vcf42.vcf.gz  # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz    # create tbi index
bcftools index example_vcf42_only_header.vcf.gz  # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:184: cd /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose 
reference bases should always be the same nucleotide ... ok
testBlocks (AlignedSegment_test.TestAlignedSegment) ... ok
check comparison functions. ... ok
testEmpty (AlignedSegment_test.TestAlignedSegment) ... ok
see issue 26 ... ok
testHashing (AlignedSegment_test.TestAlignedSegment) ... ok
build an example read. ... ok
issue 176: retrieving length without query sequence ... ok
testPositions (AlignedSegment_test.TestAlignedSegment) ... ok
see issue 62 ... ok
testStrOfEmptyRead (AlignedSegment_test.TestAlignedSegment) ... ok
check if updating fields affects other variable length data ... ok
issue 135: inplace update of sequence and quality score. ... ok
check if updating tlen works ... ok
test_get_aligned_pairs (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_hard_clipping (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_match_mismatch (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_padding (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_skip (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_skip_reference (AlignedSegment_test.TestAlignedSegment) ... ok
test_get_aligned_pairs_soft_clipping (AlignedSegment_test.TestAlignedSegment) ... ok
Test infer_query_length on M|=|X|I|D|H|S cigar ops ... ok
test_query_length_is_limited (AlignedSegment_test.TestAlignedSegment) ... ok
testAsString (AlignedSegment_test.TestAsString) ... ok
testStats (AlignedSegment_test.TestCigarStats) ... ok
testCopy (AlignedSegment_test.TestCopy) ... ok
testDeepCopy (AlignedSegment_test.TestCopy) ... ok
testAddTags (AlignedSegment_test.TestTags) ... ok
testAddTagsType (AlignedSegment_test.TestTags) ... ok
testArrayTags (AlignedSegment_test.TestTags) ... ok
testEmptyTag (AlignedSegment_test.TestTags) ... ok
testMDTagComplex (AlignedSegment_test.TestTags) ... ok
testMDTagDeletions (AlignedSegment_test.TestTags) ... ok
testMDTagInsertions (AlignedSegment_test.TestTags) ... ok
testMDTagMatchOnly (AlignedSegment_test.TestTags) ... ok
testMDTagRefSkipping (AlignedSegment_test.TestTags) ... ok
testMDTagSoftClipping (AlignedSegment_test.TestTags) ... ok
testMissingTag (AlignedSegment_test.TestTags) ... ok
testSetTag (AlignedSegment_test.TestTags) ... ok
test for tag parsing ... ok
testTagsUpdatingFloat (AlignedSegment_test.TestTags) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFetch) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFile) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFileNo) ... ok
testARQueryLength (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARcigar (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARcigarstring (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARflag (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmapq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARmrnm (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARpos (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARqual (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARquery (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARrname (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARseq (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testOpt (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testPairedBools (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testPresentOptionalFields (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testTags (AlignmentFile_test.BasicTestBAMFromFilename) ... ok
testARQueryLength (AlignmentFile_test.BasicTestCRAMFromFetch) ... Segmentation fault
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=139: cd /<<BUILDDIR>>/python-pysam-0.10.0+ds/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose 
dh_auto_test: pybuild --test -i python{version} -p 2.7 returned exit code 13
debian/rules:38: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.10.0+ds'
debian/rules:32: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-04-10T04:39:35Z

Finished
--------


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

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

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 2739
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 707
Job: python-pysam_0.10.0+ds-1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 3493
Source-Version: 0.10.0+ds-1
Space: 0
Status: failed
Version: 0.10.0+ds-1
--------------------------------------------------------------------------------
Finished at 2017-04-10T04:39:35Z
Build needed 00:00:00, 0k disc space