diff --git a/ApplicationCode/CMakeLists.txt b/ApplicationCode/CMakeLists.txt
index 88463dd4a3..0ef7757ad7 100644
--- a/ApplicationCode/CMakeLists.txt
+++ b/ApplicationCode/CMakeLists.txt
@@ -2,6 +2,10 @@ cmake_minimum_required (VERSION 2.8.12)
 
 project (ApplicationCode)
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 # Open GL
 find_package( OpenGL )
 
@@ -76,6 +80,11 @@ include_directories(
     ${CMAKE_CURRENT_BINARY_DIR}
 )
 
+################################################################################
+# Eigen
+################################################################################
+include_directories(SYSTEM ${ResInsight_SOURCE_DIR}/ThirdParty/Eigen-Subset)
+
 #############################################################################
 # Defining all the source (and header) files
 #############################################################################
@@ -232,9 +241,21 @@ if (RESINSIGHT_FOUND_HDF5)
         FileInterface/RifHdf5Reader.cpp
     )
 
+    add_definitions(-DUSE_HDF5)
+
+    if(MSVC)
+	    add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB)
+
+        include_directories(${RESINSIGHT_HDF5_DIR}/include)
+    else()
+	    add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB)
+		add_definitions(${HDF5_DEFINITIONS})
+
+		include_directories(${HDF5_INCLUDE_DIRS})
+    endif() # MSVC
+
     source_group( "FileInterface" FILES FileInterface/RifHdf5Reader.h FileInterface/RifHdf5Reader.cpp )
 
-    add_definitions(-DUSE_HDF5)
 endif()
 
 if (RESINSIGHT_ENABLE_PROTOTYPE_FEATURE_SOURING)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 88681f67f2..9f3ada9dfb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -164,10 +164,6 @@ mark_as_advanced(FORCE RESINSIGHT_ENABLE_PROTOTYPE_FEATURE_SOURING)
 if (RESINSIGHT_ENABLE_PROTOTYPE_FEATURE_SOURING)
     if(MSVC)
         if(NOT ${RESINSIGHT_HDF5_DIR} EQUAL "")
-	        add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB)
-        
-            include_directories(${RESINSIGHT_HDF5_DIR}/include)
-        
 	        list(APPEND EXTERNAL_LINK_LIBRARIES
                 ${RESINSIGHT_HDF5_DIR}/lib/hdf5.lib
                 ${RESINSIGHT_HDF5_DIR}/lib/hdf5_cpp.lib
@@ -181,10 +177,6 @@ if (RESINSIGHT_ENABLE_PROTOTYPE_FEATURE_SOURING)
     else()
         find_package(HDF5 COMPONENTS CXX)
         if (HDF5_FOUND)
-	        add_definitions(-DH5_BUILT_AS_DYNAMIC_LIB)
-		    add_definitions(${HDF5_DEFINITIONS})
-		    include_directories(${HDF5_INCLUDE_DIRS})
-
 		    list(APPEND EXTERNAL_LINK_LIBRARIES
 		        ${HDF5_LIBRARIES}
 		    )
@@ -198,7 +190,6 @@ if (RESINSIGHT_ENABLE_PROTOTYPE_FEATURE_SOURING)
 		        message( STATUS "Bundling of HDF5 libraries is enabled" )
 	        endif() # RESINSIGHT_HDF5_BUNDLE_LIBRARIES
 
-
         else()
             message( WARNING "Use of HDF5 is enabled, but no HDF5 is found." )
         endif() # HDF5_FOUND
@@ -294,11 +285,6 @@ list(APPEND THIRD_PARTY_LIBRARIES
     expressionparser
 )
 
-################################################################################
-# Eigen
-################################################################################
-include_directories(SYSTEM ThirdParty/Eigen-Subset)
-
 ################################################################################
 # clipper
 ################################################################################
diff --git a/Fwk/VizFwk/LibCore/CMakeLists.txt b/Fwk/VizFwk/LibCore/CMakeLists.txt
index b16ca5e051..3fd911b689 100644
--- a/Fwk/VizFwk/LibCore/CMakeLists.txt
+++ b/Fwk/VizFwk/LibCore/CMakeLists.txt
@@ -6,6 +6,10 @@ project(LibCore)
 # Use our strict compile flags
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  ${CEE_STRICT_CXX_FLAGS}")
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 set(CEE_HEADER_FILES
 cvfArray.h
 cvfArray.inl
diff --git a/Fwk/VizFwk/LibRender/CMakeLists.txt b/Fwk/VizFwk/LibRender/CMakeLists.txt
index 3d2871a930..78c0f2a7fc 100644
--- a/Fwk/VizFwk/LibRender/CMakeLists.txt
+++ b/Fwk/VizFwk/LibRender/CMakeLists.txt
@@ -9,7 +9,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  ${CEE_STRICT_CXX_FLAGS}")
 # For now, disable warning about unknown pragmas locally here (due to usage of OpenMP)
 # Probably need to do this more centralized whenever we use OpenMP more extensively
 if (CMAKE_COMPILER_IS_GNUCXX)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  -Wno-unknown-pragmas")
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas -Wno-deprecated -Wno-deprecated-declarations")
 endif()
 
 # For now, remove pedantic flag for OSX since it clashes with glew
diff --git a/Fwk/VizFwk/LibViewing/CMakeLists.txt b/Fwk/VizFwk/LibViewing/CMakeLists.txt
index c78e39442e..bf1ef031c5 100644
--- a/Fwk/VizFwk/LibViewing/CMakeLists.txt
+++ b/Fwk/VizFwk/LibViewing/CMakeLists.txt
@@ -6,6 +6,10 @@ project(LibViewing)
 # Use our strict compile flags
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  ${CEE_STRICT_CXX_FLAGS}")
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 set(CEE_HEADER_FILES
 cvfClipPlaneSet.h
 cvfConstantFrameRate.h
diff --git a/ThirdParty/NRLib/CMakeLists.txt b/ThirdParty/NRLib/CMakeLists.txt
index 6b0f1a261e..9b7680f67b 100644
--- a/ThirdParty/NRLib/CMakeLists.txt
+++ b/ThirdParty/NRLib/CMakeLists.txt
@@ -2,6 +2,10 @@ cmake_minimum_required (VERSION 2.8.12)
 
 project (NRLib)
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 include_directories(
        ${CMAKE_CURRENT_SOURCE_DIR}
        ${CMAKE_CURRENT_SOURCE_DIR}/nrlib
diff --git a/ThirdParty/custom-opm-flowdiag-app/CMakeLists.txt b/ThirdParty/custom-opm-flowdiag-app/CMakeLists.txt
index d54ae136a9..11db6a10df 100644
--- a/ThirdParty/custom-opm-flowdiag-app/CMakeLists.txt
+++ b/ThirdParty/custom-opm-flowdiag-app/CMakeLists.txt
@@ -2,6 +2,10 @@ cmake_minimum_required (VERSION 2.8.12)
 
 project (custom-opm-flowdiag-app)
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 include_directories(
     ../custom-opm-flowdiagnostics/opm-flowdiagnostics
     opm-flowdiagnostics-applications
diff --git a/ThirdParty/custom-opm-flowdiagnostics/CMakeLists.txt b/ThirdParty/custom-opm-flowdiagnostics/CMakeLists.txt
index 447ed4e265..f5b77781bb 100644
--- a/ThirdParty/custom-opm-flowdiagnostics/CMakeLists.txt
+++ b/ThirdParty/custom-opm-flowdiagnostics/CMakeLists.txt
@@ -2,6 +2,10 @@ cmake_minimum_required (VERSION 2.8)
 
 project (custom-opm-flowdiagnostics)
 
+if (CMAKE_COMPILER_IS_GNUCXX)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-deprecated-declarations")
+endif()
+
 include_directories(
     opm-flowdiagnostics
 )