From 7f8a040373f74a400f0900b048eaacae6b3f2091 Mon Sep 17 00:00:00 2001
From: Afif Elghraoui <afif@debian.org>
Date: Wed, 25 Jan 2017 22:16:07 -0800
Subject: [PATCH] Revert "provide LD_LIBRARY_PATH for run time test to avoid
 RPATH setting"

This reverts commit cd8ba39c2a2b3182decd87fcbc150595e1a6aee2.
---
 debian/patches/rpath.patch | 19 +++++++++++++++++++
 debian/rules               |  8 +++-----
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index b330796..44a34aa 100644
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -4,6 +4,15 @@ Forwarded: not-needed
 Last-Update: 2016-03-05
 --- python-pysam.orig/cy_build.py
 +++ python-pysam/cy_build.py
+@@ -57,7 +57,7 @@
+             ext._init_func(ext)
+ 
+         if not self.inplace:
+-            ext.library_dirs.append(os.path.join(self.build_lib, "pysam"))
++            pass
+ 
+         if sys.platform == 'darwin':
+             relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
 @@ -85,6 +85,5 @@
              if not ext.extra_link_args:
                  ext.extra_link_args = []
@@ -11,3 +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
+@@ -353,7 +353,6 @@
+     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",
diff --git a/debian/rules b/debian/rules
index 1534c65..45f2fff 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,12 +14,12 @@ HTSLIBDIR  := /usr/lib/$(DEB_HOST_MULTIARCH)
 export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
 export HTSLIB_INCLUDE_DIR=/usr/include
 
-#export PYBUILD_TEST_NOSE=1
+export PYBUILD_TEST_NOSE=1
 # pybuild calls nosetests as `python{version} -m nose tests`
 #
 # The "tests" argument (passed by pybuild as shown above) fails,
 # so don't pass anything:
-#export PYBUILD_TEST_ARGS=
+export PYBUILD_TEST_ARGS=
 # This is how we pass parameters to nose without command-line flags
 export NOSE_WHERE=$(CURDIR)/tests
 export NOSE_VERBOSE=2
@@ -35,9 +35,7 @@ override_dh_install: clean-tests
 	dh_install -Xtest.gtf.gz
 
 override_dh_auto_test: pysam_data.all cbcf_data.all
-	#dh_auto_test
-	dh_auto_test -- --test --system=custom \
-			--test-args='set -x; echo "{build_dir}/pysam {interpreter}"; LD_LIBRARY_PATH={build_dir}/pysam {interpreter} -m nose'
+	dh_auto_test
 
 override_dh_auto_clean:
 	dh_auto_clean
-- 
2.30.2