Do not use -isystem to add headers, as they break GCC 6's header wrapping.
See also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129

--- a/client/base/CMakeLists.txt
+++ b/client/base/CMakeLists.txt
@@ -49,7 +49,7 @@
   mutex.cc
   mysql_query_runner.cc
   show_variable_query_extractor.cc
-  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 
 TARGET_LINK_LIBRARIES(client_base mysqlclient)
--- a/client/CMakeLists.txt
+++ b/client/CMakeLists.txt
@@ -52,7 +52,7 @@
     upgrade/program.cc
   )
 ADD_COMPILE_FLAGS(
-  upgrade/program.cc COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  upgrade/program.cc COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 TARGET_LINK_LIBRARIES(mysql_upgrade mysqlclient client_base mysqlcheck_core)
 ADD_DEPENDENCIES(mysql_upgrade GenFixPrivs GenSysSchema)
--- a/client/dump/CMakeLists.txt
+++ b/client/dump/CMakeLists.txt
@@ -68,7 +68,7 @@
   ADD_COMPILE_FLAGS(
     ${BOOST_LIB_SOURCES}
     ${BOOST_THREAD_SOURCES}
-    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
     )
 
   IF(HAVE_clock_gettime_IN_rt)
@@ -163,7 +163,7 @@
 
 ADD_COMPILE_FLAGS(
   ${MYSQLPUMP_LIB_SOURCES}
-  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
   )
 
 # Files that use Boost sources that trigger compilation warnings
@@ -199,7 +199,7 @@
 )
 MYSQL_ADD_EXECUTABLE(mysqlpump  program.cc)
 ADD_COMPILE_FLAGS(
-  program.cc COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  program.cc COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 
 TARGET_LINK_LIBRARIES(mysqlpump mysqlpump_lib ${LOCAL_BOOST_LIB})
--- a/libmysqld/CMakeLists.txt
+++ b/libmysqld/CMakeLists.txt
@@ -115,7 +115,7 @@
   ../sql/item_geofunc_setops.cc
   ../sql/item_json_func.cc
   ../sql/spatial.cc
-  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 
 # Fixes "C1128: number of sections exceeded object file format limit" in MSVC /MD
--- a/sql/CMakeLists.txt
+++ b/sql/CMakeLists.txt
@@ -309,7 +309,7 @@
   item_geofunc_setops.cc
   item_json_func.cc
   spatial.cc
-  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 
 # Fixes "C1128: number of sections exceeded object file format limit" in MSVC /MD
--- a/storage/innobase/xtrabackup/src/CMakeLists.txt
+++ b/storage/innobase/xtrabackup/src/CMakeLists.txt
@@ -68,7 +68,7 @@
   ../../../../plugin/keyring/keyring_key.cc
   ../../../../plugin/keyring/buffered_file_io.cc
   ../../../../plugin/keyring/keys_container.cc
-  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+  COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
 )
 
 ADD_COMPILE_FLAGS(
--- a/unittest/gunit/CMakeLists.txt
+++ b/unittest/gunit/CMakeLists.txt
@@ -378,7 +378,7 @@
   ENDIF()
   ADD_COMPILE_FLAGS(
     ${MERGE_SMALL_TESTS}
-    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
   )
   INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
 
@@ -453,11 +453,11 @@
   ENDIF()
   ADD_COMPILE_FLAGS(
     bounded_queue-t.cc
-    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
   )
   ADD_COMPILE_FLAGS(
     pump_object_filter-t.cc
-    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -isystem ${BOOST_INCLUDE_DIR}
+    COMPILE_FLAGS -I${BOOST_PATCHES_DIR} -I${BOOST_INCLUDE_DIR}
   )
 
   FOREACH(test ${SERVER_TESTS})