Build log for python-pysam (0.15.2+ds-2) on armhf

python-pysam → 0.15.2+ds-2 → armhf → 2019-03-05 22:11:06

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04

+==============================================================================+
| python-pysam 0.15.2+ds-2 (armhf)             Tue, 05 Mar 2019 20:43:37 +0000 |
+==============================================================================+

Package: python-pysam
Version: 0.15.2+ds-2
Source Version: 0.15.2+ds-2
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-feb04252-f0dd-40f5-b3ad-63ff63fbc8fc' 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 [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 27s (920 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 1385 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main python-pysam 0.15.2+ds-2 (dsc) [2528 B]
Get:2 http://172.17.0.1/private buster-staging/main python-pysam 0.15.2+ds-2 (tar) [1371 kB]
Get:3 http://172.17.0.1/private buster-staging/main python-pysam 0.15.2+ds-2 (diff) [11.7 kB]
Fetched 1385 kB in 0s (6690 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pysam-ZjOzae/python-pysam-0.15.2+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pysam-ZjOzae' 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-XqpZyf/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-XqpZyf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-XqpZyf/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2845 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 krb5-locales libexpat1
  libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 libnss-systemd libpam-systemd 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 42 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14031 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 (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
Filtered Build-Depends: debhelper (>= 11~), dh-exec, dh-python, libhts-dev (>= 1.9), zlib1g-dev, python-all-dev, python-setuptools, cython (>= 0.23), python3-all-dev, python3-setuptools, cython3 (>= 0.23), tabix, samtools (>= 1.9), bcftools (>= 1.9), python-pytest, python3-pytest
dpkg-deb: building package 'sbuild-build-depends-python-pysam-dummy' in '/<<BUILDDIR>>/resolver-XqpZyf/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-XqpZyf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Sources [596 B]
Get:5 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ Packages [664 B]
Fetched 2593 B in 1s (3571 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session 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 libdeflate0 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
  libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib
  librtmp1 libsigsegv2 libssh2-1 libtool libuchardet0 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-pathlib2 python-pkg-resources python-pluggy python-py python-pytest
  python-scandir 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 python3.7 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 python3.7-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 libdeflate0 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
  libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib
  librtmp1 libsigsegv2 libssh2-1 libtool libuchardet0 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-pathlib2 python-pkg-resources python-pluggy python-py python-pytest
  python-scandir 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 python3.7 python3.7-dev python3.7-minimal
  samtools sbuild-build-depends-python-pysam-dummy tabix zlib1g-dev
0 upgraded, 110 newly installed, 0 to remove and 42 not upgraded.
Need to get 119 MB of archives.
After this operation, 263 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-XqpZyf/apt_archive ./ sbuild-build-depends-python-pysam-dummy 0.invalid.0 [948 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 libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.16~rc1-1 [394 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.16~rc1-1 [1090 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.16~rc1-1 [1844 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.16~rc1-1 [304 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpython3.7-minimal armhf 3.7.2-2 [582 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf python3.7-minimal armhf 3.7.2-2 [1455 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.7.2-1 [36.6 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libpython3.7-stdlib armhf 3.7.2-2 [1662 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3.7 armhf 3.7.2-2 [323 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.7.2-1 [20.0 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.7.2-1 [61.5 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-10 [254 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 0.29.2-2 [1277 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf cython3 armhf 0.29.2-2 [1299 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [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 1.1.1-1 [19.7 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.1-1 [13.0 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.176-1 [158 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 2.58.3-1 [1077 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 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 libcroco3 armhf 0.6.12-3 [132 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1 [1015 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.2-3 [76.7 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.2-3 [142 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180927 [95.8 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.6-1 [127 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-10 [4284 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.16~rc1-1 [872 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpython2.7-dev armhf 2.7.16~rc1-1 [30.8 MB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpython2-dev armhf 2.7.15-4 [20.9 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpython-dev armhf 2.7.15-4 [20.9 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpython-all-dev armhf 2.7.15-4 [1060 B]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpython3.7 armhf 3.7.2-2 [1252 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libpython3.7-dev armhf 3.7.2-2 [47.2 MB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpython3-dev armhf 3.7.2-1 [20.1 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpython3-all-dev armhf 3.7.2-1 [1064 B]
Get:78 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.15-4 [1044 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.16~rc1-1 [290 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf python2-dev armhf 2.7.15-4 [1212 B]
Get:81 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.15-4 [1188 B]
Get:82 http://172.17.0.1/private buster-staging/main armhf python-all-dev armhf 2.7.15-4 [1064 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-scandir armhf 1.9.0-2 [17.1 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf python-pathlib2 all 2.3.3-1 [18.3 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.8.0-1 [182 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf python-pluggy all 0.8.0-1 [20.5 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf python-py all 1.7.0-2 [86.5 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf python-pytest all 3.10.1-2 [243 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 40.8.0-1 [382 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf python3-all armhf 3.7.2-1 [1060 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf python3.7-dev armhf 3.7.2-2 [510 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf python3-dev armhf 3.7.2-1 [1260 B]
Get:98 http://172.17.0.1/private buster-staging/main armhf python3-all-dev armhf 3.7.2-1 [1060 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 40.8.0-1 [153 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 1.7.0-2 [86.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf python3-pytest all 3.10.1-2 [243 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf python3-setuptools all 40.8.0-1 [306 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.9-4 [397 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.9-10 [239 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23.1 [25.1 kB]
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Selecting previously unselected package sbuild-build-depends-python-pysam-dummy.
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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 (1.36.0-2) ...
Setting up mime-support (3.62) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-6) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up libpsl5:armhf (0.20.2-2) ...
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Setting up libglib2.0-0:armhf (2.58.3-1) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
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 libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.35-2) ...
Setting up libmagic1:armhf (1:5.35-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
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 (5.2.4-1) ...
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 (2.7.16~rc1-1) ...
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Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.64.0-1) ...
Setting up groff-base (1.22.4-2) ...
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Setting up intltool-debian (0.35.0+20060710.5) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpython3.7-dev:armhf (3.7.2-2) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up tabix (1.9-10) ...
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Setting up libhts2:armhf (1.9-10) ...
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Setting up python3-more-itertools (4.2.0-1) ...
Setting up python3-pkg-resources (40.8.0-1) ...
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Setting up python2-dev (2.7.15-4) ...
Setting up python3-attr (18.2.0-1) ...
Setting up cython3 (0.29.2-2) ...
Setting up samtools (1.9-4) ...
Setting up python3-lib2to3 (3.7.2-3) ...
Setting up bcftools (1.9-1) ...
Setting up python3-distutils (3.7.2-3) ...
Setting up python (2.7.15-4) ...
Setting up python3-atomicwrites (1.1.5-2) ...
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Setting up python-funcsigs (1.0.2-4) ...
Setting up python3-setuptools (40.8.0-1) ...
Setting up python-pathlib2 (2.3.3-1) ...
Setting up dh-python (3.20180927) ...
Setting up python-all (2.7.15-4) ...
Setting up python-setuptools (40.8.0-1) ...
Setting up python-py (1.7.0-2) ...
Setting up python-more-itertools (4.2.0-1) ...
Setting up python3-dev (3.7.2-1) ...
Setting up python-pytest (3.10.1-2) ...
Setting up python-all-dev (2.7.15-4) ...
Setting up python3-all (3.7.2-1) ...
Setting up python3-all-dev (3.7.2-1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Setting up debhelper (12.1) ...
Setting up dh-exec (0.23.1) ...
Setting up sbuild-build-depends-python-pysam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-20+rpi1 gcc-8_8.2.0-20+rpi1 libc6-dev_2.28-6+rpi1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 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_3.5.46 bash_5.0-2 bcftools_1.9-1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-20+rpi1 cython_0.29.2-2 cython3_0.29.2-2 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-exec_0.23.1 dh-python_3.20180927 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-20+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-6-base_6.5.0-1+rpi1 gcc-8_8.2.0-20+rpi1 gcc-8-base_8.2.0-20+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.2 libasan5_8.2.0-20+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-20+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-6+rpi1 libc-dev-bin_2.28-6+rpi1 libc6_2.28-6+rpi1 libc6-dev_2.28-6+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.2.0-20+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.2 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.176-1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.2.0-20+rpi1 libgcc1_1:8.2.0-20+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-20+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnss-systemd_240-5+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-5+rpi1 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-all-dev_2.7.15-4 libpython-dev_2.7.15-4 libpython-stdlib_2.7.15-4 libpython2-dev_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7_2.7.16~rc1-1 libpython2.7-dev_2.7.16~rc1-1 libpython2.7-minimal_2.7.16~rc1-1 libpython2.7-stdlib_2.7.16~rc1-1 libpython3-all-dev_3.7.2-1 libpython3-dev_3.7.2-1 libpython3-stdlib_3.7.2-1 libpython3.7_3.7.2-2 libpython3.7-dev_3.7.2-2 libpython3.7-minimal_3.7.2-2 libpython3.7-stdlib_3.7.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-20+rpi1 libstdc++6_8.2.0-20+rpi1 libsystemd0_240-5+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.2.0-20+rpi1 libuchardet0_0.0.6-3 libudev1_240-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+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_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 multiarch-support_2.28-6+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-all_2.7.15-4 python-all-dev_2.7.15-4 python-atomicwrites_1.1.5-2 python-attr_18.2.0-1 python-dev_2.7.15-4 python-funcsigs_1.0.2-4 python-minimal_2.7.15-4 python-more-itertools_4.2.0-1 python-pathlib2_2.3.3-1 python-pkg-resources_40.8.0-1 python-pluggy_0.8.0-1 python-py_1.7.0-2 python-pytest_3.10.1-2 python-scandir_1.9.0-2 python-setuptools_40.8.0-1 python-six_1.12.0-1 python2_2.7.15-4 python2-dev_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.16~rc1-1 python2.7-dev_2.7.16~rc1-1 python2.7-minimal_2.7.16~rc1-1 python3_3.7.2-1 python3-all_3.7.2-1 python3-all-dev_3.7.2-1 python3-atomicwrites_1.1.5-2 python3-attr_18.2.0-1 python3-dev_3.7.2-1 python3-distutils_3.7.2-3 python3-lib2to3_3.7.2-3 python3-minimal_3.7.2-1 python3-more-itertools_4.2.0-1 python3-pkg-resources_40.8.0-1 python3-pluggy_0.8.0-1 python3-py_1.7.0-2 python3-pytest_3.10.1-2 python3-setuptools_40.8.0-1 python3-six_1.12.0-1 python3.7_3.7.2-2 python3.7-dev_3.7.2-2 python3.7-minimal_3.7.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 samtools_1.9-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-pysam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-5+rpi1 systemd-sysv_240-5+rpi1 sysvinit-utils_2.93-6 tabix_1.9-10 tar_1.30+dfsg-5 tzdata_2018i-1 udev_240-5+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 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 Wed Feb 20 10:46:46 2019 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./python-pysam_0.15.2+ds-2.dsc
dpkg-source: info: extracting python-pysam in /<<BUILDDIR>>/python-pysam-0.15.2+ds
dpkg-source: info: unpacking python-pysam_0.15.2+ds.orig.tar.xz
dpkg-source: info: unpacking python-pysam_0.15.2+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip_test_remote.patch
dpkg-source: info: applying skip_test_needing_missing_data.patch
dpkg-source: info: applying spelling
dpkg-source: info: applying test_index_not_compression

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-feb04252-f0dd-40f5-b3ad-63ff63fbc8fc
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package python-pysam
dpkg-buildpackage: info: source version 0.15.2+ds-2
dpkg-buildpackage: info: source distribution unstable
 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-0.15.2+ds/tests/pysam_data'
rm -fr *.bam *.bai *.fai *.pileup* *.cram \
*~ calDepth *.dSYM pysam_*.sam \
ex2.sam ex2.sam.gz ex1.sam \
with_md.sam.gz \
*.fq.gz
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/cbcf_data'
rm -f *.gz *.tbi *.csi *.bcf
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+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 # which deletes files tested
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
rm -rf .pytest_cache/
dh clean --with python2,python3 --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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: python3.7 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-0.15.2+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-0.15.2+ds'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules build-arch
dh build-arch --with python2,python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base: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: python3.7 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-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.2+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/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/include/samtools/win32
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libchtslib.o build/temp.linux-armhf-2.7/pysam/htslib_util.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcsamtools.o build/temp.linux-armhf-2.7/samtools/bam.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-2.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-2.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-2.7/samtools/dict.c.pysam.o build/temp.linux-armhf-2.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-2.7/samtools/padding.c.pysam.o build/temp.linux-armhf-2.7/samtools/phase.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-2.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-2.7/samtools/sample.c.pysam.o build/temp.linux-armhf-2.7/samtools/samtools.pysam.o build/temp.linux-armhf-2.7/samtools/stats.c.pysam.o build/temp.linux-armhf-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-2.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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 -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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcftools.o build/temp.linux-armhf-2.7/bcftools/HMM.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-2.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-2.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-2.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-2.7/bcftools/em.c.pysam.o build/temp.linux-armhf-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-2.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/main.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-2.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-2.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-2.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-2.7/bcftools/version.c.pysam.o build/temp.linux-armhf-2.7/bcftools/filter.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration]
   bcftools_set_stderr(__pyx_t_9);
   ^~~~~~~~~~~~~~~~~~~
   samtools_set_stderr
pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration]
     bcftools_set_stdout_fn(__pyx_t_12);
     ^~~~~~~~~~~~~~~~~~~~~~
     samtools_set_stdout_fn
pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration]
     bcftools_set_stdout(__pyx_t_9);
     ^~~~~~~~~~~~~~~~~~~
     samtools_set_stdout
pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration]
     bcftools_set_optind(1);
     ^~~~~~~~~~~~~~~~~~~
     samtools_set_optind
pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration]
     __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
                      samtools_main
pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration]
   bcftools_unset_stderr();
   ^~~~~~~~~~~~~~~~~~~~~
   samtools_unset_stderr
pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration]
     bcftools_unset_stdout();
     ^~~~~~~~~~~~~~~~~~~~~
     samtools_unset_stdout
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:11401:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             return PyInt_FromLong((long) value);
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcutils.c:5821:7: 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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcutils.o build/temp.linux-armhf-2.7/pysam/pysam_util.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcsamtools -lcbcftools -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcutils.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:29332:127: 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:619:
/usr/include/htslib/sam.h:686:96: 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:27585:16: 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:13687:20: 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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-armhf-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’:
pysam/libcalignedsegment.c:14226:10: 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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:8631:27: 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:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13729:39: 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, 976, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14099:43: 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, 1005, __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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabix.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:32813:3: 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:618:
/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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbcf.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcbgzf.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+ds -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libctabixproxies.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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.74’:
pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __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-LSEXuZ/python2.7-2.7.16~rc1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/pysam/libcvcf.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/usr/lib/arm-linux-gnueabihf -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam -lz -lhts -lchtslib -lcutils -o /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/pysam/libcvcf.so -Wl,-rpath,$ORIGIN
I: pybuild base:217: /usr/bin/python3 setup.py build 
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/Pileup.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/bcftools.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/samtools.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/utils.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/version.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/config.py -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include
copying pysam/include/__init__.py -> /<<BUILDDIR>>/python-pysam-0.15.2+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/libcalignedsegment.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcalignmentfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcbcftools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcfaidx.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamfile.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcsamtools.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabix.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libctabixproxies.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcutils.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libcvcf.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/libchtslib.pxd -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/cbcftools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/csamtools_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/htslib_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_stream.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
copying pysam/pysam_util.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_endian.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_lpileup.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bam_plbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/bedidx.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_header.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sam_opts.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/sample.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/samtools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/stats_isize.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/tmp_file.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
copying samtools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/HMM.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bam_sample.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/bin.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/call.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/convert.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/filter.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/gvcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/hclust.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kheap.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/kmin.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/mw.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/ploidy.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/prob1.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/rbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/regidx.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/vcmp.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/version.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
copying bcftools/config.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/bcftools
creating /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/include/samtools/win32
Fixing /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/Pileup.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/__init__.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/bcftools.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/samtools.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/utils.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/version.py /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/config.py /<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -o /<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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.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/bam2depth.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_aux.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_cat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_color.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_flags.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_import.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_index.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_markdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_mate.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_md.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_plbuf.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/bam_reheader.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_sort.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_split.c.pysam.o build/temp.linux-armhf-3.7/samtools/bam_stat.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamshuf.c.pysam.o build/temp.linux-armhf-3.7/samtools/bamtk.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedcov.c.pysam.o build/temp.linux-armhf-3.7/samtools/bedidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/cut_target.c.pysam.o build/temp.linux-armhf-3.7/samtools/dict.c.pysam.o build/temp.linux-armhf-3.7/samtools/faidx.c.pysam.o build/temp.linux-armhf-3.7/samtools/padding.c.pysam.o build/temp.linux-armhf-3.7/samtools/phase.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_header.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_opts.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_utils.c.pysam.o build/temp.linux-armhf-3.7/samtools/sam_view.c.pysam.o build/temp.linux-armhf-3.7/samtools/sample.c.pysam.o build/temp.linux-armhf-3.7/samtools/samtools.pysam.o build/temp.linux-armhf-3.7/samtools/stats.c.pysam.o build/temp.linux-armhf-3.7/samtools/stats_isize.c.pysam.o build/temp.linux-armhf-3.7/samtools/tmp_file.c.pysam.o build/temp.linux-armhf-3.7/samtools/lz4/lz4.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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 -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/python-pysam-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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 -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-0.15.2+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/HMM.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bam_sample.c.pysam.o build/temp.linux-armhf-3.7/bcftools/bcftools.pysam.o build/temp.linux-armhf-3.7/bcftools/bin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ccall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/consensus.c.pysam.o build/temp.linux-armhf-3.7/bcftools/convert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/csq.c.pysam.o build/temp.linux-armhf-3.7/bcftools/em.c.pysam.o build/temp.linux-armhf-3.7/bcftools/gvcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/hclust.c.pysam.o build/temp.linux-armhf-3.7/bcftools/kmin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/main.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/mpileup.c.pysam.o build/temp.linux-armhf-3.7/bcftools/ploidy.c.pysam.o build/temp.linux-armhf-3.7/bcftools/prob1.c.pysam.o build/temp.linux-armhf-3.7/bcftools/regidx.c.pysam.o build/temp.linux-armhf-3.7/bcftools/reheader.c.pysam.o build/temp.linux-armhf-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tabix.c.pysam.o build/temp.linux-armhf-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcall.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcffilter.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfindex.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfisec.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfquery.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfroh.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsom.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfsort.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfstats.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcfview.c.pysam.o build/temp.linux-armhf-3.7/bcftools/vcmp.c.pysam.o build/temp.linux-armhf-3.7/bcftools/version.c.pysam.o build/temp.linux-armhf-3.7/bcftools/filter.c.pysam.o -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-arm-linux-gnueabihf -o /<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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_pf_5pysam_9libcutils_8_pysam_dispatch’:
pysam/libcutils.c:6089:3: warning: implicit declaration of function ‘bcftools_set_stderr’; did you mean ‘samtools_set_stderr’? [-Wimplicit-function-declaration]
   bcftools_set_stderr(__pyx_t_9);
   ^~~~~~~~~~~~~~~~~~~
   samtools_set_stderr
pysam/libcutils.c:6233:5: warning: implicit declaration of function ‘bcftools_set_stdout_fn’; did you mean ‘samtools_set_stdout_fn’? [-Wimplicit-function-declaration]
     bcftools_set_stdout_fn(__pyx_t_12);
     ^~~~~~~~~~~~~~~~~~~~~~
     samtools_set_stdout_fn
pysam/libcutils.c:6244:5: warning: implicit declaration of function ‘bcftools_set_stdout’; did you mean ‘samtools_set_stdout’? [-Wimplicit-function-declaration]
     bcftools_set_stdout(__pyx_t_9);
     ^~~~~~~~~~~~~~~~~~~
     samtools_set_stdout
pysam/libcutils.c:6999:5: warning: implicit declaration of function ‘bcftools_set_optind’; did you mean ‘samtools_set_optind’? [-Wimplicit-function-declaration]
     bcftools_set_optind(1);
     ^~~~~~~~~~~~~~~~~~~
     samtools_set_optind
pysam/libcutils.c:7078:22: warning: implicit declaration of function ‘bcftools_main’; did you mean ‘samtools_main’? [-Wimplicit-function-declaration]
     __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
                      ^~~~~~~~~~~~~
                      samtools_main
pysam/libcutils.c:7147:3: warning: implicit declaration of function ‘bcftools_unset_stderr’; did you mean ‘samtools_unset_stderr’? [-Wimplicit-function-declaration]
   bcftools_unset_stderr();
   ^~~~~~~~~~~~~~~~~~~~~
   samtools_unset_stderr
pysam/libcutils.c:7183:5: warning: implicit declaration of function ‘bcftools_unset_stdout’; did you mean ‘samtools_unset_stdout’? [-Wimplicit-function-declaration]
     bcftools_unset_stdout();
     ^~~~~~~~~~~~~~~~~~~~~
     samtools_unset_stdout
pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’:
pysam/libcutils.c:526:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   #define PyInt_FromLong               PyLong_FromLong
                                        ^~~~~~~~~~~~~~~
pysam/libcutils.c:5821:7: 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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:29332:127: 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:619:
/usr/include/htslib/sam.h:686:96: 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:27585:16: 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:13687:20: 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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:14226:10: 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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:8631:27: 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:13697:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:13729:39: 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, 976, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:14099:43: 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, 1005, __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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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:32813:3: 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:618:
/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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+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-0.15.2+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/samtools/lz4 -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/bcftools -I/<<BUILDDIR>>/python-pysam-0.15.2+ds/pysam -I/<<BUILDDIR>>/python-pysam-0.15.2+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.79’:
pysam/libcvcf.c:24828:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __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-0.15.2+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-0.15.2+ds/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<BUILDDIR>>/python-pysam-0.15.2+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-0.15.2+ds/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-arm-linux-gnueabihf.so -Wl,-rpath,$ORIGIN
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds'
cd tests/pysam_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/pysam_data'
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz
[mpileup] 1 samples in 1 input files
gunzip < ex1.sam.gz > ex1.sam
samtools index ex1.bam
samtools view -h ex1.bam | gzip > ex2.sam.gz
gunzip < ex2.sam.gz > ex2.sam
samtools view -bS ex2.sam > ex2.bam
samtools index ex2.bam
samtools calmd --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz
[bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8
[bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5
[bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5
[bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5
[bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5
[bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4
[bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3
[bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3
[bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3
[bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5
[bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3
[bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0
[bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8
[bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2
[bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5
[bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4
[bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2
[bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2
[bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1
[bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1
[bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4
[bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1
[bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1
[bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3
[bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5
[bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5
[bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4
[bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6
[bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4
[bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4
[bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5
[bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4
[bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4
[bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4
[bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7
[bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4
[bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3
[bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4
[bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6
[bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5
[bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1
[bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5
[bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2
[bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4
[bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3
[bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1
[bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1
[bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3
gunzip < with_md.sam.gz > with_md.sam
samtools view -bS with_md.sam > with_md.bam
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
samtools index with_md.bam
samtools view -buS ex2.sam > uncompressed.bam
samtools view -bS example_dash_in_chr.sam > example_dash_in_chr.bam
samtools view -bS test_mapped_unmapped.sam > test_mapped_unmapped.bam
samtools view -bS softclip.sam > softclip.bam
samtools view -bS example_empty_with_header.sam > example_empty_with_header.bam
samtools view -bS tag_bug.sam > tag_bug.bam
samtools view -bS ex10.sam > ex10.bam
samtools view -bS example_aligned_pairs.sam > example_aligned_pairs.bam
samtools view -bS example_empty_header.sam > example_empty_header.bam
samtools view -bS test_unaligned.sam > test_unaligned.bam
samtools view -bS ex9_fail.sam > ex9_fail.bam
samtools view -bS issue100.sam > issue100.bam
samtools view -bS ex5.sam > ex5.bam
samtools view -bS example_reverse_complement.sam > example_reverse_complement.bam
samtools view -bS ex4.sam > ex4.bam
samtools view -bS rg_with_tab.sam > rg_with_tab.bam
samtools view -bS ex_spliced.sam > ex_spliced.bam
samtools view -bS ex9_nofail.sam > ex9_nofail.bam
samtools view -bS example_btag.sam > example_btag.bam
samtools view -bS test_query_position.sam > test_query_position.bam
touch tmp.list
samtools import tmp.list example_unmapped_reads_no_sq.sam example_unmapped_reads_no_sq.bam
rm -f tmp.list
samtools view -bS ex6.sam > ex6.bam
samtools view -bS example_user_header.sam > example_user_header.bam
samtools view -bS ex8.sam > ex8.bam
samtools view -bS ex3.sam > ex3.bam
samtools index example_dash_in_chr.bam
samtools index test_mapped_unmapped.bam
samtools index softclip.bam
samtools index example_empty_with_header.bam
samtools index tag_bug.bam
samtools index ex10.bam
samtools index example_aligned_pairs.bam
samtools index example_empty_header.bam
samtools index test_unaligned.bam
samtools index ex9_fail.bam
samtools index issue100.bam
samtools index ex5.bam
samtools index example_reverse_complement.bam
samtools index ex4.bam
samtools index rg_with_tab.bam
samtools index ex_spliced.bam
samtools index ex9_nofail.bam
samtools index example_btag.bam
samtools index test_query_position.bam
samtools index example_unmapped_reads_no_sq.bam
samtools index ex6.bam
samtools index example_user_header.bam
samtools index ex8.bam
samtools index ex3.bam
samtools view -bC -T ex1.fa ex1.sam > ex1.cram
samtools view -bC -T ex1.fa ex2.sam > ex2.cram
samtools view -bC -T ex1.fa ex3.sam > ex3.cram
samtools index ex1.cram
samtools index ex2.cram
samtools index ex3.cram
cp ex1.bam example_bai.bam
samtools index example_bai.bam
mv example_bai.bam.bai example_bai.bai
head -c 124000 ex2.bam > ex2_truncated.bam
grep "^@" ex2.sam | samtools view -Sb - > empty.bam
samtools index empty.bam
cp ex1.bam explicit_index.bam
cp ex1.cram explicit_index.cram
gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz
bgzip < ex1.fa > ex1.fa.gz
samtools faidx ex1.fa.gz
cp ex1.bam ex1_csi.bam
samtools index -c ex1_csi.bam
rm with_md.sam
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/pysam_data'
cd tests/cbcf_data && /usr/bin/make all
make[2]: Entering directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/cbcf_data'
bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz
tabix -p vcf example_vcf42_withcontigs.vcf.gz    # create tbi index
bcftools index example_vcf42_withcontigs.vcf.gz  # create csi index
bgzip < example_vcf40.vcf > example_vcf40.vcf.gz
tabix -p vcf example_vcf40.vcf.gz    # create tbi index
bcftools index example_vcf40.vcf.gz  # create csi index
bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz
tabix -p vcf gnomad_fixed.vcf.gz    # create tbi index
bcftools index gnomad_fixed.vcf.gz  # create csi index
bgzip < gnomad.vcf > gnomad.vcf.gz
tabix -p vcf gnomad.vcf.gz    # create tbi index
bcftools index gnomad.vcf.gz  # create csi index
bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz
tabix -p vcf missing_genotypes.vcf.gz    # create tbi index
bcftools index missing_genotypes.vcf.gz  # create csi index
bgzip < example_vcf42.vcf > example_vcf42.vcf.gz
tabix -p vcf example_vcf42.vcf.gz    # create tbi index
bcftools index example_vcf42.vcf.gz  # create csi index
bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz
tabix -p vcf example_vcf42_only_header.vcf.gz    # create tbi index
bcftools index example_vcf42_only_header.vcf.gz  # create csi index
bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf
bcftools index example_vcf42_withcontigs.bcf
bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf
bcftools index example_vcf40.bcf
bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools index gnomad_fixed.bcf
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
bcftools view -O b gnomad.vcf.gz -o gnomad.bcf
bcftools index gnomad.bcf
bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf
bcftools index missing_genotypes.bcf
bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf
bcftools index example_vcf42.bcf
bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf
bcftools index example_vcf42_only_header.bcf
make[2]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds/tests/cbcf_data'
dh_auto_test
I: pybuild base:217: cd /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
============================= test session starts ==============================
platform linux2 -- Python 2.7.16rc1, pytest-3.10.1, py-1.7.0, pluggy-0.8.0 -- /usr/bin/python2.7
cachedir: .pytest_cache
rootdir: /<<BUILDDIR>>/python-pysam-0.15.2+ds, inifile: setup.cfg
collecting ... collected 926 items

tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED
tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED
tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED
tests/AlignedSegment_test.py::TestCigar::testCigar PASSED
tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED
tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED
tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED
tests/AlignedSegment_test.py::TestTags::testAddTags PASSED
tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED
tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED
tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED
tests/AlignedSegment_test.py::TestTags::testLongTags PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED
tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED
tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED
tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile PASSED
tests/AlignedSegment_test.py::TestTags::testSetTag PASSED
tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED
tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED
tests/AlignedSegment_test.py::TestCopy::testCopy PASSED
tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection FAILED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED
tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED
tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED
tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED
tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED
tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED
tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED
tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED
tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_KoWa_f
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_dHEjLb
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_XJQFWr
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_aeMeV1
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575
/<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_uq0px4
PASSED
tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_k0acbD
PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED
tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED
tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope PASSED
tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED
tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal SKIPPED
tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal SKIPPED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED
tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED
tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED
tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED
tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED
tests/AlignmentFile_test.py::TestIO::testHead PASSED
tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED
tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED
tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED
tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED
tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED
tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED
tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED
tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED
tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED
tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED
tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED
tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file missing_directory/new_file.bam
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED
tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED
tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED
tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED
tests/AlignmentFile_test.py::TestClipping::testClipping PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED
tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED
tests/AlignmentFile_test.py::TestContextManager::testManager PASSED
tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED
tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED
tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
[E::hts_open_format] Failed to open file exdoesntexist.bam
[E::hts_open_format] Failed to open file exdoesntexist.sam
PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED
tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED
tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED
tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::testBAMWholeFile PASSED
tests/AlignmentFile_test.py::TestDeNovoConstructionUserTags::test_pass_if_reads_binary_equal PASSED
tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED
tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED
tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED
tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED
tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED
tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
[W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused
PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED
tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED
tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED
tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED
tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED
tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED
tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED
tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED
tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file missing_file
PASSED
tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM [W::hts_idx_load2] The index file is older than the data file: /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/ex1.bam.bai
PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED
tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED
tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED
tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED
tests/AlignmentFile_test.py::TestHeader1000Genomes::testRead PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam PASSED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED
tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED
tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED
tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing SKIPPED
tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED
tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED
tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G
PASSED
tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED
tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED
tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file missing_file.vcf
PASSED
tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file missing_file.vcf.gz
PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED
tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED
tests/VariantFile_test.py::TestHeader::testIterator PASSED
tests/VariantFile_test.py::TestHeader::testStr PASSED
tests/VariantFile_test.py::TestParsing::testAlleles PASSED
tests/VariantFile_test.py::TestParsing::testAlt PASSED
tests/VariantFile_test.py::TestParsing::testChrom PASSED
tests/VariantFile_test.py::TestParsing::testFilter PASSED
tests/VariantFile_test.py::TestParsing::testFormat PASSED
tests/VariantFile_test.py::TestParsing::testId PASSED
tests/VariantFile_test.py::TestParsing::testInfo PASSED
tests/VariantFile_test.py::TestParsing::testPos PASSED
tests/VariantFile_test.py::TestParsing::testQual PASSED
tests/VariantFile_test.py::TestParsing::testRef PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED
tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED
tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED
tests/VariantFile_test.py::TestParsing::testStart PASSED
tests/VariantFile_test.py::TestParsing::testStop PASSED
tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED
tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED
tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
(0, 0)
FAILED
tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED
tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult PASSED
tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED
tests/compile_test.py::BAMTest::testCount PASSED
tests/compile_test.py::GTFTest::testCount PASSED
tests/faidx_test.py::TestFastaFile::testFetch PASSED
tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED
tests/faidx_test.py::TestFastaFile::testLength PASSED
tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED
tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED
tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED
tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED
tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastq::testManager PASSED
tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED
tests/faidx_test.py::TestFastqFileFastq::testManager PASSED
tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED
tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED
tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED
tests/faidx_test.py::TestFastxFileFasta::testManager PASSED
tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED
tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED
tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED
tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED
tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED
tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED
tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED
tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED
tests/samtools_test.py::SamtoolsTest::testStatements PASSED
tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED
tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED
tests/samtools_test.py::TestReturnType::testReturnValueData PASSED
tests/samtools_test.py::TestReturnType::testReturnValueString PASSED
tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED
tests/samtools_test.py::StdoutTest::testSaveStdout PASSED
tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED
tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED
tests/samtools_test.py::PysamTest::testStatements PASSED
tests/samtools_test.py::PysamTest::testUsage SKIPPED
tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting [W::bcf_hdr_check_sanity] GL should be declared as Number=G
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'CallSetAC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CallSetAC2' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED
tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'refseq.name' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'refseq.positionType' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [W::bcf_hdr_parse] Could not parse header line: #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
[E::bcf_hdr_parse] Could not parse the header, sample line not found
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'sumGLbyD' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'MMLQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AF1' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'CI95' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP4' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'MQ' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'PV4' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'GQ' is not defined in the header, assuming Type=String
[W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED
tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse_format] FORMAT 'GT' is not defined in the header, assuming Type=String
PASSED
tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED
tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED
tests/tabix_test.py::TestCompression::testCompression PASSED
tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionSam::testCompression PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionBed::testCompression PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testCompression PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED
tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED
tests/tabix_test.py::TestGZFile::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED
tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED
tests/tabix_test.py::TestIterationWithComments::testAll PASSED
tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED
tests/tabix_test.py::TestIterationWithComments::testHeader PASSED
tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED
tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED
tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED
tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED
tests/tabix_test.py::TestIterationWithComments::testReopening PASSED
tests/tabix_test.py::TestIterators::testClosedFile PASSED
tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED
tests/tabix_test.py::TestIterators::testIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED
tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED
tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED
tests/tabix_test.py::TestBed::testRead PASSED
tests/tabix_test.py::TestBed::testWrite PASSED
tests/tabix_test.py::TestVCFFromTabix::testRead PASSED
tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED
tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED
tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.)
PASSED
tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED
tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED
tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED
tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED
tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED
tests/tabix_test.py::TestMultipleIterators::testScope PASSED
tests/tabix_test.py::TestContextManager::testManager PASSED
tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED
tests/tabixproxies_test.py::TestParser::testCopy PASSED
tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestParser::testRead PASSED
tests/tabixproxies_test.py::TestParser::testUnset PASSED
tests/tabixproxies_test.py::TestParser::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::testCopy PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGTF::testRead PASSED
tests/tabixproxies_test.py::TestGTF::testUnset PASSED
tests/tabixproxies_test.py::TestGTF::testWrite PASSED
tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::testCopy PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED
tests/tabixproxies_test.py::TestGFF3::testRead PASSED
tests/tabixproxies_test.py::TestGFF3::testUnset PASSED
tests/tabixproxies_test.py::TestGFF3::testWrite PASSED
tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED
tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED
tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED
tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED
tests/test_samtools_python.py::test_bedcov_split_lines PASSED
tests/test_samtools_python.py::test_idxstats_parse PASSED
tests/test_samtools_python.py::test_bedcov PASSED

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

self = <AlignedSegment_test.TestSetTagGetTag testMethod=test_set_tag_with_automated_type_detection>

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

tests/AlignedSegment_test.py:1213: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignedSegment_test.py:1164: in check_tag
    a.set_tag(tag, value, value_type=value_type)
pysam/libcalignedsegment.pyx:2232: in pysam.libcalignedsegment.AlignedSegment.set_tag
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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

pysam/libcalignedsegment.pyx:2311: ValueError
_________ TestSetTagsGetTag.test_set_tag_with_automated_type_detection _________

self = <AlignedSegment_test.TestSetTagsGetTag testMethod=test_set_tag_with_automated_type_detection>

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

tests/AlignedSegment_test.py:1213: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
tests/AlignedSegment_test.py:1242: in check_tag
    a.set_tags([(tag, value, value_type)])
pysam/libcalignedsegment.pyx:2577: in pysam.libcalignedsegment.AlignedSegment.set_tags
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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

pysam/libcalignedsegment.pyx:422: ValueError
_____________________ TestSettingRecordValues.testGenotype _____________________

self = <VariantFile_test.TestSettingRecordValues testMethod=testGenotype>

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

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

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

pysam/libcbcf.pyx:588: TypeError
=============================== warnings summary ===============================
/usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367
  /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/_compile_test.pyx
    tree = Parsing.p_module(s, pxd, full_module_name)

.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator
  /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1459: UserWarning: no BGZF EOF marker; file may be truncated
    ignore_truncation=True)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
======== 3 failed, 906 passed, 17 skipped, 2 warnings in 499.90 seconds ========
E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-pysam-0.15.2+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests
dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13
make[1]: *** [debian/rules:32: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.2+ds'
make: *** [debian/rules:24: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-03-05T22:11:01Z

Finished
--------


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

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

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 4182
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 1011
Job: python-pysam_0.15.2+ds-2
Machine Architecture: armhf
Package: python-pysam
Package-Time: 5244
Source-Version: 0.15.2+ds-2
Space: 0
Status: failed
Version: 0.15.2+ds-2
--------------------------------------------------------------------------------
Finished at 2019-03-05T22:11:01Z
Build needed 00:00:00, 0k disc space
Raspbian Package Auto-Building

Build log for python-pysam (0.15.2+ds-2) on armhf
