diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5eb017b38..a33acc4ca 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -208,7 +208,7 @@ if(APPLE)
   endif()
 endif(APPLE)
 
-include_directories(${Boost_INCLUDE_DIRS})
+include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
 link_directories(${Boost_LIBRARY_DIRS})
 
 include_directories(${RDKit_CodeDir})
@@ -287,7 +287,7 @@ else(RDK_TEST_COVERAGE)
  if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
    # We don't on C_FLAGS warnings to keep Avalon compiling quiet
    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-array-bounds -fPIC")
-   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra")
+   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-unused-local-typedef -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC")
  endif()
 endif(RDK_TEST_COVERAGE)
 
diff --git a/Code/GraphMol/QueryOps.h b/Code/GraphMol/QueryOps.h
index 99b0cfe6c..5039f9a7c 100644
--- a/Code/GraphMol/QueryOps.h
+++ b/Code/GraphMol/QueryOps.h
@@ -20,7 +20,9 @@
 #include <Query/Query.h>
 
 #ifdef RDK_THREADSAFE_SSS
+#include <RDGeneral/BoostStartInclude.h>
 #include <boost/thread/mutex.hpp>
+#include <RDGeneral/BoostEndInclude.h>
 #endif
 
 namespace RDKit {
diff --git a/Code/RDGeneral/BoostStartInclude.h b/Code/RDGeneral/BoostStartInclude.h
index 4f978d328..d71d436c2 100644
--- a/Code/RDGeneral/BoostStartInclude.h
+++ b/Code/RDGeneral/BoostStartInclude.h
@@ -58,6 +58,7 @@
 #pragma GCC diagnostic ignored "-Wmissing-field-initializers"
 #pragma GCC diagnostic ignored "-Wsign-compare"
 #pragma GCC diagnostic ignored "-Wconversion"
+#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
 #elif defined(__HP_cc) || defined(__HP_aCC)
 /* Hewlett-Packard C/aC++. ---------------------------------- */
 
diff --git a/Code/RDGeneral/Invariant.h b/Code/RDGeneral/Invariant.h
index 4c99eab56..be9f1a683 100644
--- a/Code/RDGeneral/Invariant.h
+++ b/Code/RDGeneral/Invariant.h
@@ -24,7 +24,9 @@
 #ifdef RDDEBUG
 // Enable RDDEBUG for testing whether rdcast
 //  conversions are within numerical limits
+#include <RDGeneral/BoostStartInclude.h>
 #include <boost/numeric/conversion/cast.hpp>
+#include <RDGeneral/BoostEndInclude.h>
 #endif
 //
 // What if no invariant method is defined?
diff --git a/Code/RDGeneral/RDThreads.h b/Code/RDGeneral/RDThreads.h
index d7bfb1561..cc636723c 100644
--- a/Code/RDGeneral/RDThreads.h
+++ b/Code/RDGeneral/RDThreads.h
@@ -11,8 +11,9 @@
 #ifndef RDTHREADS_H_2015
 #define RDTHREADS_H_2015
 
+#include <RDGeneral/Invariant.h>
+
 #ifdef RDK_THREADSAFE_SSS
-#include "RDGeneral/Invariant.h"
 #include <RDGeneral/BoostStartInclude.h>
 #include <boost/thread.hpp>
 #include <RDGeneral/BoostEndInclude.h>
diff --git a/External/INCHI-API/inchi.cpp b/External/INCHI-API/inchi.cpp
index 7c7eb79c7..44688e71b 100644
--- a/External/INCHI-API/inchi.cpp
+++ b/External/INCHI-API/inchi.cpp
@@ -67,13 +67,15 @@
 #include <stack>
 #include <set>
 #include "inchi.h"
-#include <boost/foreach.hpp>
-#include <boost/tuple/tuple.hpp>
 #include <algorithm>
 
+#include <RDGeneral/BoostStartInclude.h>
+#include <boost/foreach.hpp>
+#include <boost/tuple/tuple.hpp>
 #if RDK_TEST_MULTITHREADED
 #include <boost/thread.hpp>
 #endif
+#include <RDGeneral/BoostEndInclude.h>
 
 namespace RDKit {
 namespace {