Fixing RPATHs, addresses #37

BIC-MNI · Jan 6, 2016 · 3248a1d · 3248a1d
1 parent 267e615
commit 3248a1d
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Showing 14 changed files with 53 additions and 20 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,8 +6,8 @@ cmake_minimum_required(VERSION 2.8)
 
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MAJOR 1)
 SET(MINC_TOOLKIT_PACKAGE_VERSION_MINOR 0)
-SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 07)
-SET(MINC_TOOLKIT_RELEASE_DATE "20150714")
+SET(MINC_TOOLKIT_PACKAGE_VERSION_PATCH 08)
+SET(MINC_TOOLKIT_RELEASE_DATE "20160107")
 
 SET(MINC_TOOLKIT_VERSION_FULL "${MINC_TOOLKIT_PACKAGE_VERSION_MAJOR}.${MINC_TOOLKIT_PACKAGE_VERSION_MINOR}.${MINC_TOOLKIT_PACKAGE_VERSION_PATCH}-${MINC_TOOLKIT_RELEASE_DATE}")
 
@@ -61,7 +61,17 @@ AssureOutOfSourceBuilds(minc-toolkit)
 SET(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR} CACHE PATH "Install path prefix, prepended onto install directories.")
 SET(CPACK_SET_DESTDIR    ON)
 SET(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
-SET(CPACK_STRIP_FILES ON)
+SET(CPACK_STRIP_FILES    ON)
+
+
+# RPATH magick
+#SET(MACOSX_RPATH ON)
+SET(CMAKE_SKIP_RPATH OFF)
+SET(CMAKE_SKIP_BUILD_RPATH  FALSE)
+SET(CMAKE_SKIP_INSTALL_RPATH FALSE)
+SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}")
+SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
 
 # superbuild options
 OPTION(MT_BUILD_LITE         "Build lite version of minc-toolkit, without ITK or visual tools" OFF)
@@ -97,15 +107,19 @@ SET(MINC_TEST_ENVIRONMENT
  "PATH=${CMAKE_CURRENT_BINARY_DIR}:${CMAKE_CURRENT_BINARY_DIR}/N3:${CMAKE_CURRENT_BINARY_DIR}/classify:${CMAKE_CURRENT_BINARY_DIR}/minctools/progs:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/mincblur:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/make_phantom:${CMAKE_CURRENT_BINARY_DIR}/mni_autoreg/minctracc:$ENV{PATH};PERL5LIB=${CMAKE_SOURCE_DIR}/mni-perllib:${CMAKE_CURRENT_BINARY_DIR}/mni-perllib/perl:${CMAKE_CURRENT_BINARY_DIR}/perl-modules:$ENV{PERL5LIB}"
 )
 
-# for superbuild
-IF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
-  SET(USE_SUPERBUILD OFF)
-ELSE(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
-  INCLUDE(ExternalProject)
-  SET(USE_SUPERBUILD ON)
-  INCLUDE(ConfigureExternalProjects)
-ENDIF(USE_SYSTEM_ZLIB AND USE_SYSTEM_NETCDF AND USE_SYSTEM_HDF5  AND USE_SYSTEM_PCRE  AND USE_SYSTEM_GSL AND USE_SYSTEM_FFTW3F AND USE_SYSTEM_ITK)
+LIST(APPEND MINC_TEST_ENVIRONMENT "PERL5LIB=${CMAKE_SOURCE_DIR}/mni-perllib:${CMAKE_CURRENT_BINARY_DIR}/mni-perllib/perl:${CMAKE_CURRENT_BINARY_DIR}/perl-modules:$ENV{PERL5LIB}")
+
+IF(APPLE)
+  LIST(APPEND MINC_TEST_ENVIRONMENT "DYLD_LIBRARY_PATH=${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}:${CMAKE_CURRENT_BINARY_DIR}/libminc:$ENV{DYLD_LIBRARY_PATH}")
+ELSE(APLLE)
+  LIST(APPEND MINC_TEST_ENVIRONMENT "LD_LIBRARY_PATH=${SUPERBUILD_STAGING_PREFIX}/${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}:${CMAKE_CURRENT_BINARY_DIR}/libminc:$ENV{DYLD_LIBRARY_PATH}")
+ENDIF(APPLE)
 
+
+# for superbuild
+SET(USE_SUPERBUILD ON)
+INCLUDE(ExternalProject)
+INCLUDE(ConfigureExternalProjects)
 SET(SUPERBUILD_STAGING_PREFIX ${CMAKE_BINARY_DIR}/external)
 
 # required packages

diff --git a/Display b/Display
diff --git a/Register b/Register
diff --git a/arguments b/arguments
diff --git a/bicpl b/bicpl
diff --git a/cmake-modules/BuildANTS.cmake b/cmake-modules/BuildANTS.cmake
@@ -36,6 +36,10 @@ macro(build_ANTS ANTS_location install_prefix staging_prefix)
         -DCMAKE_EXE_LINKER_FLAGS=${CMAKE_EXE_LINKER_FLAGS}
         -DCMAKE_MODULE_LINKER_FLAGS=${CMAKE_MODULE_LINKER_FLAGS}
         -DCMAKE_SHARED_LINKER_FLAGS=${CMAKE_SHARED_LINKER_FLAGS}
+        -DCMAKE_SKIP_RPATH:BOOL=OFF
+        -DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
+        -DMACOSX_RPATH:BOOL=ON
+        -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
         ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
     INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
     INSTALL_DIR ${staging_prefix}/${install_prefix}

diff --git a/cmake-modules/BuildBICGL.cmake b/cmake-modules/BuildBICGL.cmake
@@ -35,6 +35,10 @@ macro(build_bicgl bicgl_location install_prefix staging_prefix)
         -DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
         -DCMAKE_C_COMPILER:FILEPATH=${BICGL_C_COMPILER}
         -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+        -DCMAKE_SKIP_RPATH:BOOL=OFF
+        -DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
+        -DMACOSX_RPATH:BOOL=ON
+        -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
         ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
     INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
     INSTALL_DIR ${staging_prefix}/${install_prefix}

diff --git a/cmake-modules/BuildC3D.cmake b/cmake-modules/BuildC3D.cmake
@@ -41,6 +41,10 @@ macro(build_C3D C3D_location install_prefix staging_prefix)
         -DCMAKE_EXE_LINKER_FLAGS=${CMAKE_EXE_LINKER_FLAGS}
         -DCMAKE_MODULE_LINKER_FLAGS=${CMAKE_MODULE_LINKER_FLAGS}
         -DCMAKE_SHARED_LINKER_FLAGS=${CMAKE_SHARED_LINKER_FLAGS}
+        -DCMAKE_SKIP_RPATH:BOOL=OFF
+        -DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
+        -DMACOSX_RPATH:BOOL=ON
+        -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
         ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
     INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix}
     INSTALL_DIR ${staging_prefix}/${install_prefix}

diff --git a/cmake-modules/BuildITKv3.cmake b/cmake-modules/BuildITKv3.cmake
@@ -40,7 +40,6 @@ macro(build_itkv3 install_prefix staging_prefix)
     CMAKE_ARGS
         -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
         -DBUILD_SHARED_LIBS:BOOL=${ITK_SHARED_LIBRARY}
-        -DCMAKE_SKIP_RPATH:BOOL=YES
         -DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
         -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
         -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
@@ -56,6 +55,10 @@ macro(build_itkv3 install_prefix staging_prefix)
         -DITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=ON
         -DITK_USE_TRANSFORM_IO_FACTORIES:BOOL=ON
         -DITK_LEGACY_REMOVE:BOOL=OFF
+        -DCMAKE_SKIP_RPATH:BOOL=OFF
+        -DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
+        -DMACOSX_RPATH:BOOL=ON
+        -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
         -DUUID_INCLUDE_DIR:PATH= # to avoid dependecy on libuuid for now
         -DUUID_LIBRARY:FILEPATH= # to avoid dependecy on libuuid for now
         -DKWSYS_USE_MD5:BOOL=ON # Required by SlicerExecutionModel

diff --git a/cmake-modules/BuildZLIB.cmake b/cmake-modules/BuildZLIB.cmake
@@ -12,6 +12,7 @@ if(APPLE)
   list(APPEND CMAKE_OSX_EXTERNAL_PROJECT_ARGS
     -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
     -DCMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}
+    -DMACOSX_RPATH:BOOL=ON
     -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
   )
 endif()
@@ -32,6 +33,9 @@ ExternalProject_Add(ZLIB
       -DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}
       -DCMAKE_C_FLAGS:STRING=-fPIC ${CMAKE_C_FLAGS}
       -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+      -DCMAKE_SKIP_RPATH:BOOL=OFF
+      -DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF
+      -DCMAKE_INSTALL_RPATH:PATH=${install_prefix}/lib${LIB_SUFFIX}
   INSTALL_COMMAND $(MAKE) install DESTDIR=${staging_prefix} 
   INSTALL_DIR ${staging_prefix}/${install_prefix}
 )

diff --git a/libminc b/libminc
diff --git a/minctools b/minctools
diff --git a/mni_autoreg b/mni_autoreg
diff --git a/oobicpl b/oobicpl
+42 −0		ChangeLog
+103 −59		Documentation/register.1
+21 −22		Functionality/Include/main_struct.h
+12 −6		Functionality/slices/colour_map.c
+49 −37		Functionality/slices/create_slice.c
+3 −3		Functionality/slices/cursor.c
+126 −17		Functionality/slices/set_volume.c
+12 −12		Functionality/slices/slices.c
+7 −7		Functionality/tags/objects.c
+7 −4		Functionality/tags/tag_transform.c
+2 −2		Register_resample/register_resample.c
+5 −1		User_interface/Include/User_interface_prototypes.h
+4 −5		User_interface/colour_popup/colour_selection.c
+43 −3		User_interface/event_callbacks/slice_events.c
+23 −34		User_interface/main/initialize.c
+45 −11		User_interface/main/main.c
+7 −3		User_interface/print_popup/print.c
+13 −4		User_interface/quit_popup/quit.c
+2 −2		User_interface/slices/slices.c
+17 −4		User_interface/widget_instances/merged_interface.c
+1 −1		User_interface/widget_instances/volume_interface.c
+16 −4		User_interface/widgets/buttons.c
+55 −50		User_interface/windows/xsect.c
+6 −0		common_include.h
+14 −1		global_variables.h
+6 −3		CMakeLists.txt
+8 −0		ChangeLog
+516 −0		Documentation/mni_obj_format.tex
+68 −59		Images/rgb_io_none.c
+49 −10		Include/bicpl/vol_prototypes.h
+81 −78		Numerical/histogram.c
+132 −24		Volumes/create_slice.c
+28 −18		Volumes/interpolate.c
+570 −27		Volumes/render.c
+2 −2		tools/dump_points.c
+1 −1		tools/dump_polygons.c
+4 −3		tools/objconcat.c
+0 −1		.gitignore
+24 −0		.travis.yml
+1 −0		AUTHORS
+39 −9		CMakeLists.txt
+40 −1		ChangeLog
+0 −153		Makefile.am
+3 −0		NEWS
+0 −20		autogen.sh
+6 −0		brew/brew_install.sh
+9 −0		brew/hdf5.rb
+9 −0		brew/netcdf.rb
+4 −0		config.h.cmake
+0 −62		configure.ac
+4 −0		ezminc/CMakeLists.txt
+225 −192		ezminc/minc_1_rw.cpp
+3 −0		ezminc/minc_1_rw.h
+2 −0		ezminc/minc_io_exceptions.h
+6 −6		libsrc/dim_conversion.c
+41 −15		libsrc/hdf_convenience.c
+39 −25		libsrc/image_conversion.c
+11 −0		libsrc/minc.h
+6 −6		libsrc/minc_compat.c
+129 −0		libsrc/minc_config.c
+21 −13		libsrc/minc_config.h
+22 −22		libsrc/minc_convenience.c
+5 −7		libsrc/minc_error.c
+3 −1		libsrc/minc_error.h
+1 −0		libsrc/minc_private.h
+22 −22		libsrc/minc_simple.c
+123 −119		libsrc/netcdf_convenience.c
+3 −3		libsrc/value_conversion.c
+25 −25		libsrc/voxel_loop.c
+26 −0		libsrc2/hyper.c
+65 −18		libsrc2/m2util.c
+16 −0		libsrc2/minc2_api.h
+2 −2		libsrc2/minc2_defs.h
+6 −6		libsrc2/minc2_error.c
+1 −0		libsrc2/minc2_private.h
+38 −1		libsrc2/volprops.c
+79 −36		libsrc2/volume.c
+50 −4		testdir/CMakeLists.txt
+332 −0		testdir/icv_vec.c
+1 −1		testdir/minc.c
+425 −242		testdir/minc2-hyper-test.c
+74 −10		testdir/minc2-label-test.c
+1 −1		testdir/minc_types.c
+509 −0		testdir/volume_test.c
+4 −1		volume_io/Include/volume_io/vol_io_prototypes.h
+2 −0		volume_io/MNI_formats/gen_xfs.c
+1 −1		volume_io/Prog_utils/alloc.c
+3 −20		volume_io/Prog_utils/time.c
+57 −18		volume_io/Volumes/input_mgh.c
+3 −3		volume_io/Volumes/input_mnc.c
+3 −2		volume_io/Volumes/input_mnc2.c
+80 −10		volume_io/Volumes/input_nifti.c
+12 −1		volume_io/Volumes/input_volume.c
+16 −16		volume_io/Volumes/output_mnc.c
+140 −19		volume_io/Volumes/volumes.c
+7 −7		volume_io/example/convert_volume_to_byte.c
+23 −23		mincblur/gradmag_volume.c
+2 −2		minctracc/Optimize/amoeba.c