diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7af219281..3fc08c349 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -60,7 +60,7 @@ ENDIF(APPLE)
 setup_hpp_project()
 
 add_required_dependency("eigen3 >= 3.0.0")
-include_directories(${EIGEN3_INCLUDE_DIRS})
+include_directories(SYSTEM ${EIGEN3_INCLUDE_DIRS})
 
 # Add a cache variable to allow not compiling and running tests
 set (RUN_TESTS TRUE CACHE BOOL "compile and run unit tests")
diff --git a/cmake b/cmake
index ecaf20c28..441552634 160000
--- a/cmake
+++ b/cmake
@@ -1 +1 @@
-Subproject commit ecaf20c28c8ce33de312fbd812f88037cf995b73
+Subproject commit 441552634e4c427956be7b2834a6bbf894b24f0c
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 523a1974a..3ffd16884 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -83,7 +83,7 @@ set(${LIBRARY_NAME}_SOURCES
   )
 
 # Declare boost include directories
-include_directories(${Boost_INCLUDE_DIRS})
+include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
 link_directories(${Boost_LIBRARY_DIRS})
 
 add_library(${LIBRARY_NAME}
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 046d21ae9..88ae18961 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -18,7 +18,7 @@ macro(add_fcl_test test_name)
 endmacro(add_fcl_test)
 
 include_directories(${CMAKE_CURRENT_BINARY_DIR})
-include_directories(${Boost_INCLUDE_DIRS})
+include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
 
 
 add_fcl_test(test_fcl_math test_fcl_math.cpp)