Show fewer warnings on Visual Studio

7509c2bf · Peter Eastman · 300566f3 · 7509c2bf · 7509c2bf · 7509c2bf
Commit 7509c2bf authored Aug 12, 2015 by Peter Eastman
20 changed files
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -120,7 +120,11 @@ IF (APPLE AND (NOT PNACL))
    SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
 ELSE (APPLE AND (NOT PNACL))
    IF (MSVC OR ANDROID OR PNACL)
-        SET(EXTRA_COMPILE_FLAGS)
+        IF (MSVC)
+            SET(EXTRA_COMPILE_FLAGS "/W 2")
+        ELSE (MSVC)
+            SET(EXTRA_COMPILE_FLAGS)
+        ENDIF (MSVC)
    ELSE (MSVC OR ANDROID OR PNACL)
        SET(EXTRA_COMPILE_FLAGS "-msse2")
    ENDIF (MSVC OR ANDROID OR PNACL)
@@ -287,6 +291,9 @@ IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
        SET(EXTRA_LINK_FLAGS "${EXTRA_LINK_FLAGS} -Wl,--no-as-needed -lrt")
    ENDIF (NOT ANDROID)
 ENDIF (CMAKE_SYSTEM_NAME MATCHES "Linux")
+IF (MSVC)
+    SET(EXTRA_LINK_FLAGS)
+ENDIF (MSVC)

 IF(OPENMM_BUILD_SHARED_LIB)
    ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})

--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -28,7 +28,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
        SET_TARGET_PROPERTIES(${EX_ROOT}
            PROPERTIES
            PROJECT_LABEL "Example - ${EX_ROOT}"
-            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
        TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
    ENDIF (OPENMM_BUILD_SHARED_LIB)
@@ -40,7 +40,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
        SET_TARGET_PROPERTIES(${EX_STATIC}
            PROPERTIES
            PROJECT_LABEL "Example - ${EX_STATIC}"
-            LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+            LINK_FLAGS "${EXTRA_LINK_FLAGS}"
            COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
        TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
    ENDIF (OPENMM_BUILD_STATIC_LIB)
@@ -62,7 +62,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
            SET_TARGET_PROPERTIES(${EX_ROOT}
                PROPERTIES
                PROJECT_LABEL "Example C - ${EX_ROOT}"
-                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
            TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
            ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
@@ -77,7 +77,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
            SET_TARGET_PROPERTIES(${EX_STATIC}
                PROPERTIES
                PROJECT_LABEL "Example C - ${EX_STATIC}"
-                LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
+                LINK_FLAGS "${EXTRA_LINK_FLAGS}"
                COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
            TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
            ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)

--- a/platforms/cpu/sharedTarget/CMakeLists.txt
+++ b/platforms/cpu/sharedTarget/CMakeLists.txt
@@ -18,6 +18,6 @@ ENDFOREACH(file)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})

 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
--- a/platforms/cpu/staticTarget/CMakeLists.txt
+++ b/platforms/cpu/staticTarget/CMakeLists.txt
@@ -17,6 +17,6 @@ ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP

 TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB_STATIC})
 #-DPTW32_STATIC_LIB only works for the windows pthreads.
-SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
+SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
--- a/platforms/cpu/tests/CMakeLists.txt
+++ b/platforms/cpu/tests/CMakeLists.txt
@@ -23,7 +23,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    ELSE (OPENMM_BUILD_SHARED_LIB)
        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
    ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)

 ENDFOREACH(TEST_PROG ${TEST_PROGS})
--- a/platforms/cuda/sharedTarget/CMakeLists.txt
+++ b/platforms/cuda/sharedTarget/CMakeLists.txt
@@ -18,7 +18,7 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
--- a/platforms/cuda/staticTarget/CMakeLists.txt
+++ b/platforms/cuda/staticTarget/CMakeLists.txt
@@ -19,7 +19,7 @@ SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
--- a/platforms/cuda/tests/CMakeLists.txt
+++ b/platforms/cuda/tests/CMakeLists.txt
@@ -28,7 +28,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    IF (APPLE)
        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ELSE (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ENDIF (APPLE)

    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)

--- a/platforms/opencl/sharedTarget/CMakeLists.txt
+++ b/platforms/opencl/sharedTarget/CMakeLists.txt
@@ -14,6 +14,6 @@ SET_SOURCE_FILES_PROPERTIES(${CL_KERNELS_CPP} ${CL_KERNELS_H} PROPERTIES GENERAT
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})

 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_SHARED_LIBRARY")

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
--- a/platforms/opencl/staticTarget/CMakeLists.txt
+++ b/platforms/opencl/staticTarget/CMakeLists.txt
@@ -15,6 +15,6 @@ ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP

 TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB_STATIC})
 #-DPTW32_STATIC_LIB only works for the windows pthreads.
-SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
+SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_OPENCL_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")

 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
--- a/platforms/opencl/tests/CMakeLists.txt
+++ b/platforms/opencl/tests/CMakeLists.txt
@@ -25,7 +25,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    # Link with shared library
    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")

    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
    IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)

--- a/platforms/reference/tests/CMakeLists.txt
+++ b/platforms/reference/tests/CMakeLists.txt
@@ -15,7 +15,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    ELSE (OPENMM_BUILD_SHARED_LIB)
        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
    ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})

 ENDFOREACH(TEST_PROG ${TEST_PROGS})

--- a/plugins/amoeba/CMakeLists.txt
+++ b/plugins/amoeba/CMakeLists.txt
@@ -86,14 +86,14 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)

 ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")

 FILE(GLOB serialization_files  ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
 SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")

 IF(OPENMM_BUILD_STATIC_LIB)
  ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
-  SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+  SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_STATIC_LIBRARY -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)

 IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)

--- a/plugins/amoeba/platforms/cuda/CMakeLists.txt
+++ b/plugins/amoeba/platforms/cuda/CMakeLists.txt
@@ -94,7 +94,7 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)

 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)

--- a/plugins/amoeba/platforms/cuda/tests/CMakeLists.txt
+++ b/plugins/amoeba/platforms/cuda/tests/CMakeLists.txt
@@ -17,7 +17,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    IF (APPLE)
        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ELSE (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ENDIF (APPLE)
    ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
    IF (OPENMM_BUILD_CUDA_DOUBLE_PRECISION_TESTS)

--- a/plugins/amoeba/platforms/reference/CMakeLists.txt
+++ b/plugins/amoeba/platforms/reference/CMakeLists.txt
@@ -71,7 +71,7 @@ ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_AMOEBA_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")

 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)


--- a/plugins/amoeba/platforms/reference/tests/CMakeLists.txt
+++ b/plugins/amoeba/platforms/reference/tests/CMakeLists.txt
@@ -12,7 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    # Link with shared library
    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})

 ENDFOREACH(TEST_PROG ${TEST_PROGS})
--- a/plugins/amoeba/serialization/tests/CMakeLists.txt
+++ b/plugins/amoeba/serialization/tests/CMakeLists.txt
@@ -12,7 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    # All tests use shared libraries
    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_AMOEBA_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})

 ENDFOREACH(TEST_PROG ${TEST_PROGS})
--- a/plugins/cpupme/CMakeLists.txt
+++ b/plugins/cpupme/CMakeLists.txt
@@ -75,7 +75,7 @@ IF (OPENMM_BUILD_SHARED_LIB)
    IF (FFTW_THREADS_LIBRARY)
        TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${FFTW_THREADS_LIBRARY})
    ENDIF (FFTW_THREADS_LIBRARY)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")

    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
 ENDIF (OPENMM_BUILD_SHARED_LIB)
@@ -88,7 +88,7 @@ IF(OPENMM_BUILD_STATIC_LIB)
    IF (FFTW_THREADS_LIBRARY)
        TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${FFTW_THREADS_LIBRARY})
    ENDIF (FFTW_THREADS_LIBRARY)
-    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_STATIC_LIBRARY")
+    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_STATIC_LIBRARY")

    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})
 ENDIF(OPENMM_BUILD_STATIC_LIB)

--- a/plugins/cpupme/tests/CMakeLists.txt
+++ b/plugins/cpupme/tests/CMakeLists.txt
@@ -13,6 +13,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
    ELSE (OPENMM_BUILD_SHARED_LIB)
        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static)
    ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})