provide LD_LIBRARY_PATH for run time test to avoid RPATH setting

diff --git a/debian/changelog b/debian/changelog
index f42253eecf4fc13c66fcd95eec61944562432b9b..e886b01bd11aee42ca22df01ebb6271c0905cd4e 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,7 @@ python-pysam (0.10.0+ds-1) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * d/rules: Remove redundant get-orig-source target
+  * provide LD_LIBRARY_PATH for run time test to avoid RPATH setting
 
  -- Afif Elghraoui <afif@debian.org>  Mon, 23 Jan 2017 19:13:47 -0800
 

diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
index 44a34aa23ae315857714aac04a679f0dd19ecf66..b33079610c740ef71633eb3dc1caa44099cd29d8 100644 (file)
--- a/debian/patches/rpath.patch
+++ b/debian/patches/rpath.patch
@@ -4,15 +4,6 @@ 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 = []
@@ -20,13 +11,3 @@ 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 838cc31ea3dd67fb8ef38fdee6b019c7cd4a74e8..cdddf037ed230f4021707766f12d548ef99b6451 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -12,12 +12,12 @@ 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
@@ -33,7 +33,9 @@ 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
+       dh_auto_test -- --test --system=custom \
+                       --test-args='set -x; echo "{build_dir}/pysam {interpreter}"; LD_LIBRARY_PATH={build_dir}/pysam {interpreter} -m nose'
 
 override_dh_auto_clean:
        dh_auto_clean