diff --git a/Code/Mantid/MantidPlot/CMakeLists.txt b/Code/Mantid/MantidPlot/CMakeLists.txt
index 68daaff89d6fdea488c03b40bf6bba8e2d9fcfac..6314b89a3f66c3453d7097e99b98e615f199154a 100644
--- a/Code/Mantid/MantidPlot/CMakeLists.txt
+++ b/Code/Mantid/MantidPlot/CMakeLists.txt
@@ -548,7 +548,7 @@ add_custom_command ( OUTPUT ${SIP_SRC}
 )
 
 # Needed for sip.h header that can end up in a different place to to the main Python include directory
-include_directories ( ${SIP_INCLUDE_DIR} )
+include_directories ( SYSTEM ${SIP_INCLUDE_DIR} )
 # Needed for sip generated files to find includes in src
 include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} )
 
diff --git a/Code/Mantid/MantidQt/Python/CMakeLists.txt b/Code/Mantid/MantidQt/Python/CMakeLists.txt
index 0624231af29b862ae944506786baf9f0deee4902..92a7f22f8f992ec7b5177a0d6c92fbc48b0afc6d 100644
--- a/Code/Mantid/MantidQt/Python/CMakeLists.txt
+++ b/Code/Mantid/MantidQt/Python/CMakeLists.txt
@@ -49,7 +49,7 @@ add_custom_command ( OUTPUT ${SIP_SRC}
 )                     
 
 # Needed for sip.h header that can end up in a different place to to the main Python include directory
-include_directories ( ${SIP_INCLUDE_DIR} )
+include_directories ( SYSTEM ${SIP_INCLUDE_DIR} )
 
 # Needed for sip generated files to find includes in src
 include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} )
diff --git a/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt b/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
index f2af04d6f4fd3c63c5c5347edca31def4f45d1b8..0ccd2ead71b5a5445fd65dce9fe71a743b84a121 100644
--- a/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
+++ b/Code/Mantid/Vates/VatesSimpleGui/StandAloneExec/CMakeLists.txt
@@ -39,11 +39,12 @@ set( TEST_SUITES
 add_executable( ${PROJECT_NAME} ${INCLUDE_FILES} ${SOURCE_FILES} ${MOC_SRCS} )
 
 target_link_libraries( ${PROJECT_NAME}
+VatesSimpleGuiQtWidgets
+VatesSimpleGuiViewWidgets
+SYSTEM
 pqCore pqComponents pqApplicationComponents
 ${QT_LIBRARIES}
 ${MANTID_SUBPROJECT_LIBS}
-VatesSimpleGuiQtWidgets
-VatesSimpleGuiViewWidgets
 )
 
 if( SQUISH_FOUND )
diff --git a/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt b/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
index 278a8015e40de9a2a2b631f9d86a845a854ea999..6d64ce35f82cd51c06ce475048c7453d6d5bba71 100644
--- a/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
+++ b/Code/Mantid/Vates/VatesSimpleGui/ViewWidgets/CMakeLists.txt
@@ -124,15 +124,16 @@ set_property( TARGET VatesSimpleGuiViewWidgets PROPERTY FOLDER MantidVatesSimple
 
 target_link_libraries( VatesSimpleGuiViewWidgets
 VatesSimpleGuiQtWidgets
-pqApplicationComponents
-pqComponents
-${QT_LIBRARIES}
 MantidQtAPI
 VatesAPI
 ${MANTID_SUBPROJECT_LIBS}
 MantidQtSliceViewer
 MantidQtFactory
 MantidWidgets
+SYSTEM
+pqApplicationComponents
+pqComponents
+${QT_LIBRARIES}
 )
 
 # Create test file projects