Build log for python-pysam (0.14+ds-2+rpi1+b1) on armhf

python-pysam → 0.14+ds-2+rpi1+b1 → armhf → 2018-12-21 02:01:11

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| python-pysam 0.14+ds-2+rpi1+b1 (armhf)       Fri, 21 Dec 2018 01:25:30 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.14+ds-2+rpi1+b1
Source Version: 0.14+ds-2+rpi1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-03416b0c-5c0e-454e-904c-6140574d91c2' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.3 MB in 10s (2550 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-pysam.git
Please use:
git clone https://salsa.debian.org/med-team/python-pysam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2602 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main python-pysam 0.14+ds-2+rpi1 (dsc) [2668 B]
Get:2 http://172.17.0.1/private buster-staging/main python-pysam 0.14+ds-2+rpi1 (tar) [2589 kB]
Get:3 http://172.17.0.1/private buster-staging/main python-pysam 0.14+ds-2+rpi1 (diff) [10.8 kB]
Fetched 2602 kB in 0s (6567 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-TK5MNM/python-pysam-0.14+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-TK5MNM' 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-osMuz8/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-osMuz8/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-osMuz8/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9795 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
  libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
  systemd-sysv
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 39 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15795 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.7), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.7), bcftools (>= 1.7), python-pytest, python3-pytest
Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.7), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.7), bcftools (>= 1.7), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-osMuz8/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-osMuz8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Sources [599 B]
Get:5 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ Packages [660 B]
Fetched 2592 B in 0s (12.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
  libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu63
  liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1
  libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev
  libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
  libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib
  libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib
  librtmp1 libsigsegv2 libssh2-1 libtool libxml2 m4 man-db mime-support
  po-debconf python python-all python-all-dev python-atomicwrites python-attr
  python-dev python-funcsigs python-minimal python-more-itertools
  python-pkg-resources python-pluggy python-py python-pytest python-setuptools
  python-six python2 python2-dev python2-minimal python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites
  python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal
  python3-more-itertools python3-pkg-resources python3-pluggy python3-py
  python3-pytest python3-setuptools python3-six python3.6 python3.6-dev
  python3.6-minimal python3.7 python3.7-dev python3.7-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 liblzma-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl python-doc python-tk python-attr-doc
  python-funcsigs-doc subversion python-pytest-xdist python-mock
  python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc
  python3-tk python3-venv python3.6-venv python3.6-doc python3.7-venv
  python3.7-doc
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl cwltool
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bcftools bsdmainutils cython
  cython3 debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism
  dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl
  libbsd0 libcroco3 libcurl3-gnutls libelf1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts2 libicu63
  liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1
  libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev
  libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
  libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib
  libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib
  librtmp1 libsigsegv2 libssh2-1 libtool libxml2 m4 man-db mime-support
  po-debconf python python-all python-all-dev python-atomicwrites python-attr
  python-dev python-funcsigs python-minimal python-more-itertools
  python-pkg-resources python-pluggy python-py python-pytest python-setuptools
  python-six python2 python2-dev python2-minimal python2.7 python2.7-dev
  python2.7-minimal python3 python3-all python3-all-dev python3-atomicwrites
  python3-attr python3-dev python3-distutils python3-lib2to3 python3-minimal
  python3-more-itertools python3-pkg-resources python3-pluggy python3-py
  python3-pytest python3-setuptools python3-six python3.6 python3.6-dev
  python3.6-minimal python3.7 python3.7-dev python3.7-minimal samtools
  sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 113 newly installed, 0 to remove and 39 not upgraded.
Need to get 166 MB/166 MB of archives.
After this operation, 360 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-osMuz8/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-5 [394 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-5 [1089 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-5 [1844 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-5 [299 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpython3.7-minimal armhf 3.7.2~rc1-1 [582 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf python3.7-minimal armhf 3.7.2~rc1-1 [1454 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.7.1-2 [36.5 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpython3.7-stdlib armhf 3.7.2~rc1-1 [1662 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python3.7 armhf 3.7.2~rc1-1 [322 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.7.1-2 [20.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.7.1-2 [61.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.8~rc1-1 [567 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.8~rc1-1 [1382 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.62.0-1 [284 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf bcftools armhf 1.9-1 [449 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf cython armhf 0.28.4-1+b1 [1956 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf cython3 armhf 0.28.4-1+b1 [2788 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.4 [1003 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.1-1 [78.7 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.1-1 [144 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180927 [95.8 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.6-1 [127 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.15-5 [871 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libpython2.7-dev armhf 2.7.15-5 [30.8 MB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libpython2-dev armhf 2.7.15-3 [20.8 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpython-dev armhf 2.7.15-3 [20.8 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpython-all-dev armhf 2.7.15-3 [1064 B]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpython3.7 armhf 3.7.2~rc1-1 [1251 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpython3.7-dev armhf 3.7.2~rc1-1 [47.2 MB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpython3-dev armhf 3.7.1-2 [20.1 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.8~rc1-1 [1638 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libpython3.6 armhf 3.6.8~rc1-1 [1181 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpython3.6-dev armhf 3.6.8~rc1-1 [43.7 MB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpython3-all-dev armhf 3.7.1-2 [1076 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.15-3 [1044 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.15-5 [289 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf python2-dev armhf 2.7.15-3 [1216 B]
Get:81 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.15-3 [1192 B]
Get:82 http://172.17.0.1/private buster-staging/main armhf python-all-dev armhf 2.7.15-3 [1068 B]
Get:83 http://172.17.0.1/private buster-staging/main armhf python-atomicwrites all 1.1.5-2 [6808 B]
Get:84 http://172.17.0.1/private buster-staging/main armhf python-attr all 18.2.0-1 [37.2 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf python-funcsigs all 1.0.2-4 [13.7 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf python-six all 1.12.0-1 [15.7 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf python-more-itertools all 4.2.0-1 [42.3 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.6.2-1 [181 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf python-pluggy all 0.8.0-1 [20.5 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf python-py all 1.7.0-1 [86.4 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf python-pytest all 3.6.4-1 [221 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 40.6.2-1 [380 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.8~rc1-1 [245 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf python3-all armhf 3.7.1-2 [1068 B]
Get:95 http://172.17.0.1/private buster-staging/main armhf python3.7-dev armhf 3.7.2~rc1-1 [522 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf python3-dev armhf 3.7.1-2 [1260 B]
Get:97 http://172.17.0.1/private buster-staging/main armhf python3.6-dev armhf 3.6.8~rc1-1 [509 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf python3-all-dev armhf 3.7.1-2 [1076 B]
Get:99 http://172.17.0.1/private buster-staging/main armhf python3-atomicwrites all 1.1.5-2 [6892 B]
Get:100 http://172.17.0.1/private buster-staging/main armhf python3-attr all 18.2.0-1 [37.3 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf python3-six all 1.12.0-1 [15.7 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf python3-more-itertools all 4.2.0-1 [42.2 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 40.6.2-1 [152 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf python3-pluggy all 0.8.0-1 [20.6 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf python3-py all 1.7.0-1 [86.5 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf python3-pytest all 3.6.4-1 [221 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 40.6.2-1 [303 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.7-2 [365 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.7-2 [260 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23+b8 [25.3 kB]
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Unpacking sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.35.1-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-5) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.0-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libpython3.6-minimal:armhf (3.6.8~rc1-1) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.28-2) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libexpat1-dev:armhf (2.2.6-1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up bsdmainutils (11.1.2) ...
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 (2.7.15-5) ...
Setting up autopoint (0.19.8.1-9) ...
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Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.0.0-1) ...
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Setting up autoconf (2.69-11) ...
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Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libpython3.7:armhf (3.7.2~rc1-1) ...
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Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpython3.7-dev:armhf (3.7.2~rc1-1) ...
Setting up man-db (2.8.4-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up tabix (1.7-2) ...
Setting up libpython2-stdlib:armhf (2.7.15-3) ...
Setting up libpython2.7-dev:armhf (2.7.15-5) ...
Setting up python2.7-dev (2.7.15-5) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libpython3.6:armhf (3.6.8~rc1-1) ...
Setting up libpython3-dev:armhf (3.7.1-2) ...
Setting up libtool (2.4.6-6) ...
Setting up libpython3-stdlib:armhf (3.7.1-2) ...
Setting up python3.6 (3.6.8~rc1-1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3 (3.7.1-2) ...
Setting up libhts-dev:armhf (1.7-2) ...
Setting up python3-six (1.12.0-1) ...
Setting up python3-more-itertools (4.2.0-1) ...
Setting up python3-pkg-resources (40.6.2-1) ...
Setting up python3.7-dev (3.7.2~rc1-1) ...
Setting up python3-pluggy (0.8.0-1) ...
Setting up libpython3.6-dev:armhf (3.6.8~rc1-1) ...
Setting up python2 (2.7.15-3) ...
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Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up libpython3-all-dev:armhf (3.7.1-2) ...
Setting up python2-dev (2.7.15-3) ...
Setting up python3-attr (18.2.0-1) ...
Setting up cython3 (0.28.4-1+b1) ...
Setting up samtools (1.7-2) ...
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Setting up python3-lib2to3 (3.7.1-1) ...
Setting up bcftools (1.9-1) ...
Setting up python3-distutils (3.7.1-1) ...
Setting up python (2.7.15-3) ...
Setting up python3-atomicwrites (1.1.5-2) ...
Setting up libpython-dev:armhf (2.7.15-3) ...
Setting up python-atomicwrites (1.1.5-2) ...
Setting up python-attr (18.2.0-1) ...
Setting up python3-py (1.7.0-1) ...
Setting up python-dev (2.7.15-3) ...
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Setting up python-pluggy (0.8.0-1) ...
Setting up libpython-all-dev:armhf (2.7.15-3) ...
Setting up python-pkg-resources (40.6.2-1) ...
Setting up cython (0.28.4-1+b1) ...
Setting up python-six (1.12.0-1) ...
Setting up python-funcsigs (1.0.2-4) ...
Setting up python3-setuptools (40.6.2-1) ...
Setting up dh-python (3.20180927) ...
Setting up python-all (2.7.15-3) ...
Setting up python-setuptools (40.6.2-1) ...
Setting up python-py (1.7.0-1) ...
Setting up python-more-itertools (4.2.0-1) ...
Setting up python3-dev (3.7.1-2) ...
Setting up python-pytest (3.6.4-1) ...
Setting up python-all-dev (2.7.15-3) ...
Setting up python3-all (3.7.1-2) ...
Setting up python3-all-dev (3.7.1-2) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (11.5.4) ...
Setting up dh-exec (0.23+b8) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-10+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-9+rpi1 gcc-8_8.2.0-9+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 bcftools_1.9-1 binutils_2.31.1-10+rpi1 binutils-arm-linux-gnueabihf_2.31.1-10+rpi1 binutils-common_2.31.1-10+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-9+rpi1 cython_0.28.4-1+b1 cython3_0.28.4-1+b1 dash_0.5.10.2-2 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_11.5.4 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23+b8 dh-python_3.20180927 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.11-1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-9+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-9+rpi1 gcc-8-base_8.2.0-9+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.11-1 gnupg-agent_2.2.11-1 gnupg-l10n_2.2.11-1 gnupg-utils_2.2.11-1 gpg_2.2.11-1 gpg-agent_2.2.11-1 gpg-wks-client_2.2.11-1 gpg-wks-server_2.2.11-1 gpgconf_2.2.11-1 gpgsm_2.2.11-1 gpgv_2.2.11-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-10+rpi1 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-9+rpi1 libgcc1_1:8.2.0-9+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-9+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-2+b1 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1+b1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_239-15+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-15+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-all-dev_2.7.15-3 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-5 libpython2.7-dev_2.7.15-5 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libpython3-all-dev_3.7.1-2 libpython3-dev_3.7.1-2 libpython3-stdlib_3.7.1-2 libpython3.6_3.6.8~rc1-1 libpython3.6-dev_3.6.8~rc1-1 libpython3.6-minimal_3.6.8~rc1-1 libpython3.6-stdlib_3.6.8~rc1-1 libpython3.7_3.7.2~rc1-1 libpython3.7-dev_3.7.2~rc1-1 libpython3.7-minimal_3.7.2~rc1-1 libpython3.7-stdlib_3.7.2~rc1-1 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0-3 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 libsystemd0_239-15+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-9+rpi1 libudev1_239-15+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mime-support_3.61 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-all_2.7.15-3 python-all-dev_2.7.15-3 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-dev_2.7.15-3 python-funcsigs_1.0.2-4 python-minimal_2.7.15-3 python-more-itertools_4.2.0-1 python-pkg-resources_40.6.2-1 python-pluggy_0.8.0-1 python-py_1.7.0-1 python-pytest_3.6.4-1 python-setuptools_40.6.2-1 python-six_1.12.0-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-dev_2.7.15-5 python2.7-minimal_2.7.15-5 python3_3.7.1-2 python3-all_3.7.1-2 python3-all-dev_3.7.1-2 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.1-2 python3-distutils_3.7.1-1 python3-lib2to3_3.7.1-1 python3-minimal_3.7.1-2 python3-more-itertools_4.2.0-1 python3-pkg-resources_40.6.2-1 python3-pluggy_0.8.0-1 python3-py_1.7.0-1 python3-pytest_3.6.4-1 python3-setuptools_40.6.2-1 python3-six_1.12.0-1 python3.6_3.6.8~rc1-1 python3.6-dev_3.6.8~rc1-1 python3.6-minimal_3.6.8~rc1-1 python3.7_3.7.2~rc1-1 python3.7-dev_3.7.2~rc1-1 python3.7-minimal_3.7.2~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 samtools_1.7-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-15+rpi1 systemd-sysv_239-15+rpi1 sysvinit-utils_2.93-1 tabix_1.7-2 tar_1.30+dfsg-3+rpi1 tzdata_2018g-1 udev_239-15+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| 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 Mar  1 07:08:39 2018 UTC
gpgv:                using RSA key B843F038E48484EB39990C4587DEBCF2E67E9905
gpgv:                issuer "root@raspbian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.14+ds-2+rpi1.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.14+ds
dpkg-source: info: unpacking python-pysam_0.14+ds.orig.tar.gz
dpkg-source: info: unpacking python-pysam_0.14+ds-2+rpi1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying execute-linking-tests-only-when-explicitely-reque.patch
dpkg-source: info: applying xfail.patch
dpkg-source: info: applying exclude_tests_accessing_remote_http.patch
dpkg-source: info: applying skip_test_needing_missing_data.patch

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

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 0.14+ds-2+rpi1+b1

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-03416b0c-5c0e-454e-904c-6140574d91c2
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.14+ds-2+rpi1+b1
dpkg-buildpackage: info: source distribution buster-staging
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
cd tests/pysam_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c \
	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
	tests/pysam_data/ex1.fa.gz \
	tests/pysam_data/ex1.fa.gz.gzi \
	tests/pysam_data/ex1_csi.bam.csi
dh clean --with python2,python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
I: pybuild base:217: python3.6 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.6' does not exist -- can't clean it
I: pybuild base:217: python3.7 setup.py clean 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running clean
removing '/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-3.7' does not exist -- can't clean it
rm -f \
	pysam/config.py \
	pysam/config.h \
	pysam/lib*.c \
	samtools/config.h \
	bcftools/config.h
rm -rf pysam.egg-info
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:217: python2.7 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.6 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
I: pybuild base:217: python3.7 setup.py config 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running config
   dh_auto_build -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
building 'pysam.libchtslib' extension
creating build
creating build/temp.linux-armhf-2.7
creating build/temp.linux-armhf-2.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-armhf-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-armhf-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-2.7/samtools
creating build/temp.linux-armhf-2.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-armhf-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:66: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, samtools_stdout) & fputc('\n', samtools_stdout) != EOF) ret = 0;
                                                                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamtools.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-2.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-armhf-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function ‘init_data’,
    inlined from ‘main_vcfcall’ at bcftools/vcfcall.c.pysam.c:810:5:
bcftools/vcfcall.c.pysam.c:423:39: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
         args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
                                       ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:29,
                 from /usr/include/htslib/vcf.h:40,
                 from bcftools/vcfcall.c.pysam.c:34:
bcftools/vcfcall.c.pysam.c: In function ‘main_vcfcall’:
/usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here
 extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
              ^~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/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-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcftools.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcutils.pyx to pysam/libcutils.c
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-armhf-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:11184:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5647:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-armhf-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29387:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:573:
/usr/include/htslib/sam.h:594:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27640:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         (void)(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:13829:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-armhf-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:83,
                 from pysam/libcalignedsegment.c:4:
pysam/libcalignedsegment.c: In function ‘initlibcalignedsegment’:
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:2137:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libcalignedsegment.c:58576:5: note: in expansion of macro ‘__Pyx_INCREF’
     __Pyx_INCREF(((PyObject *)(&PyDict_Type)));
     ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:2137:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libcalignedsegment.c:58592:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14209:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabix.pyx to pysam/libctabix.c
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-armhf-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8640:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13911:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 965, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13943:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 966, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14313:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 995, __pyx_L1_error)
                                           ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-armhf-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-armhf-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:33134:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
                 from pysam/libcbcf.c:572:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-armhf-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In file included from /usr/include/python2.7/Python.h:83,
                 from pysam/libctabixproxies.c:4:
pysam/libctabixproxies.c: In function ‘initlibctabixproxies’:
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19206:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19209:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19236:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19264:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19318:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19321:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19378:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19432:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19435:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19466:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19484:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19502:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19520:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19538:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyFloat_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19556:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19574:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19592:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19610:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19628:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19646:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19664:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19687:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19705:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19723:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19741:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19759:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19777:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19795:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19813:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
/usr/include/python2.7/object.h:769:6: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     ((PyObject*)(op))->ob_refcnt++)
     ~^~~~~~~~~~~~~~~~
pysam/libctabixproxies.c:1237:27: note: in expansion of macro ‘Py_INCREF’
   #define __Pyx_INCREF(r) Py_INCREF(r)
                           ^~~~~~~~~
pysam/libctabixproxies.c:19831:3: note: in expansion of macro ‘__Pyx_INCREF’
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
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/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-armhf-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.71’:
pysam/libcvcf.c:24711:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __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/python2.7-7yWIbs/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3.6 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.6
creating build/temp.linux-armhf-3.6/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libchtslib.o build/temp.linux-armhf-3.6/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libchtslib.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.6/samtools
creating build/temp.linux-armhf-3.6/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.6/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:66: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, samtools_stdout) & fputc('\n', samtools_stdout) != EOF) ret = 0;
                                                                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.6/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.6/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.6/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamtools.o build/temp.linux-armhf-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/samtools.pysam.o build/temp.linux-armhf-3.6/samtools/padding.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.6/samtools/dict.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.6/samtools/stats.c.pysam.o build/temp.linux-armhf-3.6/samtools/sample.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.6/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.6/samtools/phase.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.6/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.6/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.6/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.6/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.6/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.6/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamtools.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.6/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.6/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.6/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcftools.o build/temp.linux-armhf-3.6/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.6/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.6/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.6/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.6/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.6/bcftools/main.c.pysam.o build/temp.linux-armhf-3.6/bcftools/em.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.6/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.6/bcftools/version.c.pysam.o build/temp.linux-armhf-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.6/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.6/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.6/bcftools/hclust.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcftools.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-armhf-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:480:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5647:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.6/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcutils.o build/temp.linux-armhf-3.6/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcsamtools.cpython-36m-arm-linux-gnueabihf -lcbcftools.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcutils.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:29387:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:573:
/usr/include/htslib/sam.h:594:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27640:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         (void)(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:13829:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignmentfile.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.6/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamfile.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14209:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignedsegment.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-armhf-3.6/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:8640:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13911:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 965, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13943:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 966, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14313:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 995, __pyx_L1_error)
                                           ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabix.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.6/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcfaidx.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.6/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:33134:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
                 from pysam/libcbcf.c:572:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbgzf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.6/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabixproxies.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.6/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.74’:
pysam/libcvcf.c:24711:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 873, __pyx_L1_error)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam -lz -lhts -lchtslib.cpython-36m-arm-linux-gnueabihf -lcutils.cpython-36m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcvcf.cpython-36m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.linux-armhf-3.7
creating build/temp.linux-armhf-3.7/pysam
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libchtslib.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/htslib_util.c -o build/temp.linux-armhf-3.7/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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libchtslib.o build/temp.linux-armhf-3.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating build/temp.linux-armhf-3.7/samtools
creating build/temp.linux-armhf-3.7/samtools/lz4
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcsamtools.c -o build/temp.linux-armhf-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:66: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, samtools_stdout) & fputc('\n', samtools_stdout) != EOF) ret = 0;
                                                                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_import.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sam_header.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamtools.o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating build/temp.linux-armhf-3.7/bcftools
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcbcftools.c -o build/temp.linux-armhf-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.linux-armhf-3.7/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 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcftools.o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
building 'pysam.libcutils' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcutils.c -o build/temp.linux-armhf-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:480:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5647:7: note: ‘__pyx_v_retval’ was declared here
   int __pyx_v_retval;
       ^~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/pysam_util.c -o build/temp.linux-armhf-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcutils.o build/temp.linux-armhf-3.7/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcsamtools.cpython-37m-arm-linux-gnueabihf -lcbcftools.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.linux-armhf-3.7/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:29387:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:573:
/usr/include/htslib/sam.h:594:96: note: expected ‘const bam_pileup1_t **’ {aka ‘const struct <anonymous> **’} but argument is of type ‘bam_pileup1_t **’ {aka ‘struct <anonymous> **’}
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:27640:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         (void)(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:13829:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignmentfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcsamfile.c -o build/temp.linux-armhf-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcsamfile.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14209:10: warning: ignoring return value of ‘sam_parse1’, declared with attribute warn_unused_result [-Wunused-result]
   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcalignedsegment.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libctabix.c -o build/temp.linux-armhf-3.7/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:8640:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13911:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 965, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13943:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 966, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14313:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 995, __pyx_L1_error)
                                           ^~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabix.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcfaidx.c -o build/temp.linux-armhf-3.7/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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcfaidx.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcbcf.c -o build/temp.linux-armhf-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:33134:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5,
                 from pysam/libcbcf.c:572:
/usr/include/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcbgzf.c -o build/temp.linux-armhf-3.7/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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.linux-armhf-3.7/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 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.14+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.14+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.14+ds -I/usr/include/python3.7m -c pysam/libcvcf.c -o build/temp.linux-armhf-3.7/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.73’:
pysam/libcvcf.c:24711:15: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_9 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 873, __pyx_L1_error)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.14+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.14+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -lcutils.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch --with python2,python3 --buildsystem=pybuild
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
   dh_installdirs -a -O--buildsystem=pybuild
   dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:217: /usr/bin/python setup.py install --root /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython2_2.7_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/version.py to version.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/include/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/utils.py to utils.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/__init__.py to __init__.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/Pileup.py to Pileup.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/config.py to config.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/samtools.py to samtools.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam/bcftools.py to bcftools.pyc
running install_egg_info
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing top-level names to pysam.egg-info/top_level.txt
writing dependency_links to pysam.egg-info/dependency_links.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/win/*.c'
warning: no files found matching 'htslib/win/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python-pysam/usr/lib/python2.7/dist-packages/pysam-0.14.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:217: /usr/bin/python3.6 setup.py install --root /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabixproxies.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamfile.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabix.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcfaidx.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignmentfile.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcsamtools.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbgzf.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcutils.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcf.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libchtslib.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcvcf.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcbcftools.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignedsegment.cpython-36m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.6_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/version.py to version.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/include/__init__.py to __init__.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/utils.py to utils.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/__init__.py to __init__.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/Pileup.py to Pileup.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/config.py to config.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/samtools.py to samtools.cpython-36.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam/bcftools.py to bcftools.cpython-36.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/win/*.c'
warning: no files found matching 'htslib/win/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.6/dist-packages/pysam-0.14.egg-info
Skipping SOURCES.txt
running install_scripts
I: pybuild base:217: /usr/bin/python3 setup.py install --root /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running build
running build_py
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcfaidx.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbgzf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcsamtools.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libchtslib.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools/win32
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/samtools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include
creating /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/bcftools
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.cpython-37m-arm-linux-gnueabihf.so -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
copying /<<BUILDDIR>>/python-pysam-0.14+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/version.py to version.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/include/__init__.py to __init__.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/utils.py to utils.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/__init__.py to __init__.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/Pileup.py to Pileup.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/config.py to config.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/samtools.py to samtools.cpython-37.pyc
byte-compiling /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam/bcftools.py to bcftools.cpython-37.pyc
running install_egg_info
running egg_info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/win/*.c'
warning: no files found matching 'htslib/win/*.h'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /<<BUILDDIR>>/python-pysam-0.14+ds/debian/python3-pysam/usr/lib/python3.7/dist-packages/pysam-0.14.egg-info
Skipping SOURCES.txt
running install_scripts
   debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
cd tests/pysam_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
*.fq.gz
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds/tests/cbcf_data'
find . -name "*.pyc" -delete
find . -name "*.pyxbldc" -delete
#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
find . -name "*.bai*" -delete
find . -name "*.cram*" -delete
find . -name "*.bam" -delete
rm -rf	tests/pysam_test_work \
	tests/example_htslib.gtf.gz.tbi \
	tests/log.txt \
	tests/test.bam \
	tests/_compile_test.c \
	tests/pysam_ex2.sam \
	tests/__pycache__ \
	pysam/calignmentfile.c \
	pysam/cbcf.c \
	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
	tests/pysam_data/ex1.fa.gz \
	tests/pysam_data/ex1.fa.gz.gzi \
	tests/pysam_data/ex1_csi.bam.csi
dh_install -Xtest.gtf.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.14+ds'
   dh_installdocs -a -O--buildsystem=pybuild
   dh_installchangelogs -a -O--buildsystem=pybuild
   dh_installexamples -a -O--buildsystem=pybuild
   dh_installman -a -O--buildsystem=pybuild
   dh_installcatalogs -a -O--buildsystem=pybuild
   dh_installcron -a -O--buildsystem=pybuild
   dh_installdebconf -a -O--buildsystem=pybuild
   dh_installemacsen -a -O--buildsystem=pybuild
   dh_installifupdown -a -O--buildsystem=pybuild
   dh_installinfo -a -O--buildsystem=pybuild
   dh_python2 -a -O--buildsystem=pybuild
I: dh_python2 fs:329: renaming libcalignedsegment.so to libcalignedsegment.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcalignmentfile.so to libcalignmentfile.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcbcf.so to libcbcf.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcbcftools.so to libcbcftools.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcbgzf.so to libcbgzf.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcfaidx.so to libcfaidx.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libchtslib.so to libchtslib.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcsamfile.so to libcsamfile.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcsamtools.so to libcsamtools.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libctabix.so to libctabix.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libctabixproxies.so to libctabixproxies.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcutils.so to libcutils.arm-linux-gnueabihf.so
I: dh_python2 fs:329: renaming libcvcf.so to libcvcf.arm-linux-gnueabihf.so
   dh_python3 -a -O--buildsystem=pybuild
   dh_installinit -a -O--buildsystem=pybuild
   dh_installsystemd -a -O--buildsystem=pybuild
   dh_installmenu -a -O--buildsystem=pybuild
   dh_installmime -a -O--buildsystem=pybuild
   dh_installmodules -a -O--buildsystem=pybuild
   dh_installlogcheck -a -O--buildsystem=pybuild
   dh_installlogrotate -a -O--buildsystem=pybuild
   dh_installpam -a -O--buildsystem=pybuild
   dh_installppp -a -O--buildsystem=pybuild
   dh_installudev -a -O--buildsystem=pybuild
   dh_installgsettings -a -O--buildsystem=pybuild
   dh_bugfiles -a -O--buildsystem=pybuild
   dh_ucf -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
   dh_gconf -a -O--buildsystem=pybuild
dh_gconf: Please migrate to dh_installgsettings; gconf + dh_gconf is scheduled for removal.
   dh_icons -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_usrlocal -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_installwm -a -O--buildsystem=pybuild
   dh_installxfonts -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   dh_compress -a -O--buildsystem=pybuild
   dh_fixperms -a -O--buildsystem=pybuild
   dh_missing -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   dh_shlibdeps -a -O--buildsystem=pybuild
   dh_installdeb -a -O--buildsystem=pybuild
   dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Provides} unused, but is defined
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined
dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Provides} unused, but is defined
dpkg-gencontrol: warning: package python-pysam: substitution variable ${python:Versions} unused, but is defined
   dh_md5sums -a -O--buildsystem=pybuild
   dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python-pysam-dbgsym' in '../python-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb'.
dpkg-deb: building package 'python-pysam' in '../python-pysam_0.14+ds-2+rpi1+b1_armhf.deb'.
dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.14+ds-2+rpi1+b1_armhf.deb'.
dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../python-pysam_0.14+ds-2+rpi1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-12-21T02:01:06Z

Finished
--------

I: Built successfully

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


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


python-pysam_0.14+ds-2+rpi1+b1_armhf.changes:
---------------------------------------------

Format: 1.8
Date: Thu, 01 Mar 2018 06:43:04 +0000
Source: python-pysam (0.14+ds-2+rpi1)
Binary: python-pysam python3-pysam python-pysam-tests
Binary-Only: yes
Architecture: armhf
Version: 0.14+ds-2+rpi1+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format (
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping format (
Changes:
 python-pysam (0.14+ds-2+rpi1+b1) buster-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
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 f768c0e6a96c29b175c79da954fc4a83a34d054a 1388904 python-pysam_0.14+ds-2+rpi1+b1_armhf.deb
 84ffe85471e9f9485cd866ca25dfa812aef8e174 12514652 python3-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
 1e2edf81f6791f51d2b2327f7bb80e0ae11cdd1a 1888432 python3-pysam_0.14+ds-2+rpi1+b1_armhf.deb
Checksums-Sha256:
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 5a1174428d93b06a6501315eab6375c007017f9a0fcea6ae455630992d8b54bf 8567 python-pysam_0.14+ds-2+rpi1+b1_armhf.buildinfo
 0ea85f7ec0f636e4f79deb84b9b3c0b742b508a81f688075eef95e2320a1bf27 1388904 python-pysam_0.14+ds-2+rpi1+b1_armhf.deb
 9a2bfc04a871c4c341231c0b1024904a783fdd4aa47959afd8a502362f3da808 12514652 python3-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
 f7160bc14f39a7c3dce63bd87fe931714d5e457c1e0211d4754d0a4d3ac0d494 1888432 python3-pysam_0.14+ds-2+rpi1+b1_armhf.deb
Files:
 c5807118497b2417d29149b978eaf67b 5490300 debug optional python-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
 26933580480745bec1f27d337d3dff50 8567 python optional python-pysam_0.14+ds-2+rpi1+b1_armhf.buildinfo
 29935c5ad88238ec010ab2af93248439 1388904 python optional python-pysam_0.14+ds-2+rpi1+b1_armhf.deb
 d0ea84989683d28e53962c594f40b56f 12514652 debug optional python3-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
 771dc804f745745853524769d3f79a04 1888432 python optional python3-pysam_0.14+ds-2+rpi1+b1_armhf.deb

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


python-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
-----------------------------------------------

 new Debian package, version 2.0.
 size 5490300 bytes: control archive=1156 bytes.
     920 bytes,    12 lines      control              
    1378 bytes,    13 lines      md5sums              
 Package: python-pysam-dbgsym
 Source: python-pysam (0.14+ds-2+rpi1)
 Version: 0.14+ds-2+rpi1+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 6047
 Depends: python-pysam (= 0.14+ds-2+rpi1+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for python-pysam
 Build-Ids: 4e10709f1c8bf2c022ce98fa1c681539b7d65d9e 625a55d4c6ee9cd1dcf0068f6c6017a5e84aa467 81ca9e03401de34a5a9bf6deb80860a3a95101db 9e9385e8b80df817337f0396e67e2374b7ef348e aadc6013ae4b209a1783878d888197ab48cbdc35 acbf2950004d3c58acaf86e1b06f298cd68955ee b61e9028c7aaa2ec7b9104d3c60ab3abb8f551ca e22176ef9b01035a946ecf7acfce352a645725f2 e574e34be756d783a7329f5cd592c7c49013b6c9 f3facc14cabf94e9a7f072b8ae324fa99c951e6c f59e5508085d0a7305a0ea7537b52e5d0f6e8809 f6ebbb95673e69cf197665e1dde8f8c46e158bcb fd0c79a551ad7735575a23b2b4683f296a4aef0b

drwxr-xr-x root/root         0 2018-03-01 06:43 ./
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root    149280 2018-03-01 06:43 ./usr/lib/debug/.build-id/4e/10709f1c8bf2c022ce98fa1c681539b7d65d9e.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/62/
-rw-r--r-- root/root    103652 2018-03-01 06:43 ./usr/lib/debug/.build-id/62/5a55d4c6ee9cd1dcf0068f6c6017a5e84aa467.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/81/
-rw-r--r-- root/root    297744 2018-03-01 06:43 ./usr/lib/debug/.build-id/81/ca9e03401de34a5a9bf6deb80860a3a95101db.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/9e/
-rw-r--r-- root/root    569936 2018-03-01 06:43 ./usr/lib/debug/.build-id/9e/9385e8b80df817337f0396e67e2374b7ef348e.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/aa/
-rw-r--r-- root/root    979728 2018-03-01 06:43 ./usr/lib/debug/.build-id/aa/dc6013ae4b209a1783878d888197ab48cbdc35.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/ac/
-rw-r--r-- root/root     50740 2018-03-01 06:43 ./usr/lib/debug/.build-id/ac/bf2950004d3c58acaf86e1b06f298cd68955ee.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/b6/
-rw-r--r-- root/root    612280 2018-03-01 06:43 ./usr/lib/debug/.build-id/b6/1e9028c7aaa2ec7b9104d3c60ab3abb8f551ca.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root    819120 2018-03-01 06:43 ./usr/lib/debug/.build-id/e2/2176ef9b01035a946ecf7acfce352a645725f2.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root   1090152 2018-03-01 06:43 ./usr/lib/debug/.build-id/e5/74e34be756d783a7329f5cd592c7c49013b6c9.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/f3/
-rw-r--r-- root/root    702008 2018-03-01 06:43 ./usr/lib/debug/.build-id/f3/facc14cabf94e9a7f072b8ae324fa99c951e6c.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/f5/
-rw-r--r-- root/root    209300 2018-03-01 06:43 ./usr/lib/debug/.build-id/f5/9e5508085d0a7305a0ea7537b52e5d0f6e8809.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/f6/
-rw-r--r-- root/root    242120 2018-03-01 06:43 ./usr/lib/debug/.build-id/f6/ebbb95673e69cf197665e1dde8f8c46e158bcb.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/debug/.build-id/fd/
-rw-r--r-- root/root    338272 2018-03-01 06:43 ./usr/lib/debug/.build-id/fd/0c79a551ad7735575a23b2b4683f296a4aef0b.debug
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/share/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/share/doc/
lrwxrwxrwx root/root         0 2018-03-01 06:43 ./usr/share/doc/python-pysam-dbgsym -> python-pysam


python-pysam_0.14+ds-2+rpi1+b1_armhf.deb
----------------------------------------

 new Debian package, version 2.0.
 size 1388904 bytes: control archive=3272 bytes.
     738 bytes,    16 lines      control              
    8643 bytes,    90 lines      md5sums              
     162 bytes,     9 lines   *  postinst             #!/bin/sh
     263 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: python-pysam
 Source: python-pysam (0.14+ds-2+rpi1)
 Version: 0.14+ds-2+rpi1+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 5296
 Depends: libc6 (>= 2.7), libhts2 (>= 1.7), zlib1g (>= 1:1.1.4), python (<< 2.8), python (>= 2.7~), python:any (<< 2.8), python:any (>= 2.7~)
 Section: python
 Priority: optional
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 2.

drwxr-xr-x root/root         0 2018-03-01 06:43 ./
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/python2.7/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/python2.7/dist-packages/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/lib/python2.7/dist-packages/pysam-0.14.egg-info/
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python3-pysam-dbgsym_0.14+ds-2+rpi1+b1_armhf.deb
------------------------------------------------

 new Debian package, version 2.0.
 size 12514652 bytes: control archive=1764 bytes.
    1457 bytes,    12 lines      control              
    2756 bytes,    26 lines      md5sums              
 Package: python3-pysam-dbgsym
 Source: python-pysam (0.14+ds-2+rpi1)
 Version: 0.14+ds-2+rpi1+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 13643
 Depends: python3-pysam (= 0.14+ds-2+rpi1+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for python3-pysam
 Build-Ids: 0ba5b610e5bd84c04207cba38bebee93012f3e67 0bcc95f7a2478a907cd7bc185c63f2a3f9076935 184ed1752f37c2c87106b655d06a5abcdb96b226 1e818fa67b10136913ce7de242b0ed862837728f 2cc7ab6f92f03639495504bcd0d3d16967cd1f8a 3c6ad64e5819229c487b325359885a536ff4d82a 456b66069bd9223ce4624d44f564ecce2ec1e4ee 595b503973e526e4ff9728a7564b72a92354112f 5c7737f947aae2c3a28a88ee5d839874d04cfccc 5d8d41388c899586500bc71088570bde6644dfb7 611eba42e065d309f5aa912cb95ef7b4b5bb1ab8 71d0547232018054e30b149dde08ffe907f71b76 784c62fbf78f8f5f213b4955a2f173e8174e3a03 7a792efa532cfd71bfb31c04cb013cd4f42982fb 83c62e3cb4754f9bc0766b5949252e6b656b4e74 a4507dbcda40d414f38ed183729f347e0ea05dbb acd507c940f86f1feb98c882cd3126c50a2d8e95 b89e3381842badcf41073556322636cc7f7e4c81 b8d9a337dcc0b3348af7b61356f27db1d773fabb c198d0d75ee40ee2449932136df6683bcb3e7226 cea02d2235a2458b6491d816194981b87fd86136 d395048db747ad37fbf24a5c80aa9d50d055934f da41bcf4c8bb1a765a14c46136890a9ac650a26e f448b8b9a4ea7f457bc5f0881e9c4cc6e0e99b5c f9bcd03ab1b83ea4ccf1b11e45435278c2efe968 fe62cb3c1e43e1a56262cb7905e5827818e47021

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lrwxrwxrwx root/root         0 2018-03-01 06:43 ./usr/share/doc/python3-pysam-dbgsym -> python3-pysam


python3-pysam_0.14+ds-2+rpi1+b1_armhf.deb
-----------------------------------------

 new Debian package, version 2.0.
 size 1888432 bytes: control archive=3664 bytes.
     722 bytes,    16 lines      control              
   10154 bytes,   103 lines      md5sums              
     266 bytes,    12 lines   *  postinst             #!/bin/sh
     401 bytes,    12 lines   *  prerm                #!/bin/sh
 Package: python3-pysam
 Source: python-pysam (0.14+ds-2+rpi1)
 Version: 0.14+ds-2+rpi1+b1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 10203
 Depends: libc6 (>= 2.7), libhts2 (>= 1.7), zlib1g (>= 1:1.1.4), python3 (<< 3.8), python3 (>= 3.6~), python3:any (>= 3.2~)
 Section: python
 Priority: optional
 Homepage: http://pysam.readthedocs.org/en/latest
 Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
  Pysam is a Python module for reading and manipulating Samfiles. It's a
  lightweight wrapper of the samtools C-API. Pysam also includes an interface
  for tabix.
  .
  This package installs the module for Python 3.

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-rw-r--r-- root/root      6348 2018-03-01 06:43 ./usr/share/doc/python3-pysam/copyright
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/share/lintian/
drwxr-xr-x root/root         0 2018-03-01 06:43 ./usr/share/lintian/overrides/
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| Post Build                                                                   |
+------------------------------------------------------------------------------+


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

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

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

Build Architecture: armhf
Build-Space: 237552
Build-Time: 1781
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 336
Job: python-pysam_0.14+ds-2+rpi1
Machine Architecture: armhf
Package: python-pysam
Package-Time: 2136
Source-Version: 0.14+ds-2+rpi1
Space: 237552
Status: successful
Version: 0.14+ds-2+rpi1+b1
--------------------------------------------------------------------------------
Finished at 2018-12-21T02:01:06Z
Build needed 00:35:36, 237552k disk space
Raspbian Package Auto-Building

Build log for python-pysam (0.14+ds-2+rpi1+b1) on armhf
