diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index d9233825d0eeb7e1251db30af60756e003c7a624..1ffa3bf0d63f29a90ef705ebc1297b58bae1b090 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -218,12 +218,16 @@ endif(NOT HDF5_FOUND)
 if(HDF5_FOUND)
     add_definitions( -DUSE_HDF5 )
     include_directories( ${HDF5_INCLUDE_DIRS} )
-    foreach(HDF5_LIB ${HDF5_LIBRARIES})
-        get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
-        if( ${HDF5_LIB_EXT} STREQUAL ".a" )
-            list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
-        else( )
-            list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
+    foreach(HDF5_LIB ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} )
+        if(HDF5_LIB)
+            get_filename_component( HDF5_LIB_EXT ${HDF5_LIB} EXT )
+            if(HDF5_LIB_EXT)
+                if(${HDF5_LIB_EXT} STREQUAL ".a")
+                    list(APPEND STATIC_LIBRARIES ${HDF5_LIB} )
+                else( )
+                    list(APPEND SYSTEM_SHARED_LIBS ${HDF5_LIB} )
+                endif( )
+            endif()
         endif( )
     endforeach( )
 endif( HDF5_FOUND )
@@ -274,11 +278,15 @@ if(WITH_GSL)
     message(STATUS "Using STATIC gsl libraries: ${GSL_LIBRARIES}")
 
     foreach(GSL_LIB ${GSL_LIBRARIES} )
-        get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
-        if( GSL_LIB_EXT STREQUAL ".a" )
-            list(APPEND STATIC_LIBRARIES ${GSL_LIB})
-        else()
-            list(APPEND SYSTEM_SHARED_LIBS ${GSL_LIB})
+        if(GSL_LIB)
+            get_filename_component( GSL_LIB_EXT ${GSL_LIB} EXT )
+            if(GSL_LIB_EXT)
+                if(GSL_LIB_EXT STREQUAL ".a" )
+                    list(APPEND STATIC_LIBRARIES ${GSL_LIB})
+                else()
+                    list(APPEND SYSTEM_SHARED_LIBS ${GSL_LIB})
+                endif( )
+            endif( )
         endif( )
     endforeach( )
 endif()
diff --git a/moose-core/VERSION b/moose-core/VERSION
index 4225763f8cf3bc6309bd0d3fed4f68dde69ac351..50e47c89cafc3ec95774b3110a3dba45256d0b24 100644
--- a/moose-core/VERSION
+++ b/moose-core/VERSION
@@ -1 +1 @@
-3.1.1-40-g8fe5068
\ No newline at end of file
+3.1.1
\ No newline at end of file