Actually write the "correct" installation commands, so that RPATH gets stripped

at install time.

CMakeLists.txt

@@ -58,7 +58,6 @@ if(Boost_MAJOR_VERSION EQUAL 1 AND Boost_MINOR_VERSION GREATER 45)
   set(BOOST_LIBS ${BOOST_LIBS} "boost_random")
 endif(Boost_MAJOR_VERSION EQUAL 1 AND Boost_MINOR_VERSION GREATER 45)
 
-
 # Default to debugging mode for developers.
 option(DEBUG "Compile with debugging information" ON)
 option(PROFILE "Compile with profiling information" ON)
@@ -101,7 +100,6 @@ include_directories(${LIBXML2_INCLUDE_DIRS})
 include(CMake/TargetDistclean.cmake OPTIONAL)
 
 include_directories(${CMAKE_SOURCE_DIR})
-#TODO link_directories()
 
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib/)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/)

src/mlpack/CMakeLists.txt

@@ -51,21 +51,12 @@ endforeach()
 # collected to include/.
 install(DIRECTORY ${CMAKE_BINARY_DIR}/include/mlpack DESTINATION include)
 
+# Set generated executables to be installed.  Unfortunately they must manually
+# be entered...
 install(TARGETS mlpack
-   RUNTIME DESTINATION bin
-   LIBRARY DESTINATION lib
-   ARCHIVE DESTINATION lib)
-
-# Set generated executables to be installed.
-# This will have some odd effects if the user has placed anything else in bin/,
-# but I think we can just hope that they haven't.  At least, an auto-builder
-# won't do that...
-install(DIRECTORY ${CMAKE_BINARY_DIR}/bin/
-  DESTINATION bin
-  USE_SOURCE_PERMISSIONS
-  COMPONENT mlpack
-  FILES_MATCHING
-  PATTERN *[^_test])
+  RUNTIME DESTINATION bin
+  LIBRARY DESTINATION lib
+  ARCHIVE DESTINATION lib)
 
 # For 'make test'.
 add_custom_target(test

src/mlpack/methods/emst/CMakeLists.txt

@@ -26,3 +26,4 @@ add_executable(emst
 target_link_libraries(emst
   mlpack
 )
+install(TARGETS emst RUNTIME DESTINATION bin)

src/mlpack/methods/gmm/CMakeLists.txt

@@ -26,3 +26,4 @@ add_executable(gmm
 target_link_libraries(gmm
   mlpack
 )
+install(TARGETS gmm RUNTIME DESTINATION bin)

src/mlpack/methods/hmm/CMakeLists.txt

@@ -45,3 +45,6 @@ add_executable(hmm_generate
 target_link_libraries(hmm_generate
   mlpack
 )
+
+install(TARGETS hmm_train hmm_loglik hmm_viterbi hmm_generate
+  RUNTIME DESTINATION bin)

src/mlpack/methods/kernel_pca/CMakeLists.txt

@@ -19,8 +19,7 @@ set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 add_executable(kernel_pca
   kernel_pca_main.cpp
 )
-
 target_link_libraries(kernel_pca
   mlpack
 )
-
+install(TARGETS kernel_pca RUNTIME DESTINATION bin)

src/mlpack/methods/kmeans/CMakeLists.txt

@@ -27,3 +27,4 @@ add_executable(kmeans
 target_link_libraries(kmeans
   mlpack
 )
+install(TARGETS kmeans RUNTIME DESTINATION bin)

src/mlpack/methods/lars/CMakeLists.txt

@@ -18,7 +18,7 @@ set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 add_executable(lars
   lars_main.cpp
 )
-
 target_link_libraries(lars
   mlpack
 )
+install(TARGETS lars RUNTIME DESTINATION bin)

src/mlpack/methods/linear_regression/CMakeLists.txt

@@ -23,3 +23,4 @@ add_executable(linear_regression
 target_link_libraries(linear_regression
   mlpack
 )
+install(TARGETS linear_regression RUNTIME DESTINATION bin)

src/mlpack/methods/mvu/CMakeLists.txt

@@ -24,3 +24,4 @@ add_executable(mvu
 target_link_libraries(mvu
   mlpack
 )
+install(TARGETS mvu RUNTIME DESTINATION bin)

src/mlpack/methods/naive_bayes/CMakeLists.txt

@@ -22,3 +22,4 @@ add_executable(nbc
 target_link_libraries(nbc
   mlpack
 )
+install(TARGETS nbc RUNTIME DESTINATION bin)

src/mlpack/methods/nca/CMakeLists.txt

@@ -24,3 +24,4 @@ add_executable(nca
 target_link_libraries(nca
   mlpack
 )
+install(TARGETS nca RUNTIME DESTINATION bin)

src/mlpack/methods/neighbor_search/CMakeLists.txt

@@ -36,3 +36,5 @@ add_executable(allkfn
 target_link_libraries(allkfn
   mlpack
 )
+
+install(TARGETS allknn allkfn RUNTIME DESTINATION bin)

src/mlpack/methods/pca/CMakeLists.txt

@@ -22,3 +22,4 @@ add_executable(pca
 target_link_libraries(pca
   mlpack
 )
+install(TARGETS pca RUNTIME DESTINATION bin)

src/mlpack/methods/radical/CMakeLists.txt

@@ -16,9 +16,9 @@ endforeach()
 set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
 
 add_executable(radical
-    radical_main.cpp
+  radical_main.cpp
 )
-
 target_link_libraries(radical
   mlpack
 )
+install(TARGETS radical RUNTIME DESTINATION bin)