[med-svn] [python-pysam] 01/04: Completely fix rpath issue

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-pysam.

commit c47196e7939dc762ee25187d47124a9eeeb81716
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Mar 9 22:25:29 2016 -0800

    Completely fix rpath issue
---
 debian/TODO                |  4 ----
 debian/patches/rpath.patch | 10 ++++++++++
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/debian/TODO b/debian/TODO
index 681828c..83ce291 100644
--- a/debian/TODO
+++ b/debian/TODO
@@ -1,7 +1,3 @@
-* Disable rpath setting during build
-   Cython is producing -R flags to set rpath (see it by grepping the build log).
-   This should be stopped and checked to make sure that tests still pass.
-
 * Fix tests requiring network access
    All tests should be passing now.
    The ones that fail are failing because of network access issues.
diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index b6fb0c8..61e3bea 100644
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -20,3 +20,13 @@ Last-Update: 2016-03-05
 -            ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
                                      
          build_ext.build_extension(self, ext)
+--- python-pysam.orig/setup.py
++++ python-pysam/setup.py
+@@ -348,7 +348,6 @@
+     shared_htslib_sources +
+     os_c_files,
+     library_dirs=htslib_library_dirs,
+-    runtime_library_dirs=htslib_library_dirs,
+     include_dirs=["pysam", "."] + include_os + htslib_include_dirs,
+     libraries=external_htslib_libraries,
+     language="c",

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