Completely fix rpath issue

diff --git a/debian/TODO b/debian/TODO
index 681828cab1b2aded80d4da472cbc858018924d22..83ce29124bc75657706deb07422e6008391e7862 100644 (file)
--- 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 b6fb0c8e78dfaacb2358585576cce99a47f12b07..61e3beac999c982e69d499694da18d5268b6eea1 100644 (file)
--- 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",