-pedantic shouldn't change something from OK into an error, but it was doing so for redeclaration of a declaration from a system header with a mismatched exception specification. And whether we are strict about things in system headers should be controlled by -Wsystem-headers.

Tested x86_64-pc-linux-gnu, applying to trunk.
commit 8c029a40a7d4348c432f09eb2512a485cfe9bda8
Author: Jason Merrill <ja...@redhat.com>
Date:   Tue May 26 11:47:27 2015 -0400

    	* decl.c (check_redeclaration_exception_specification): Depend on
    	-Wsystem-headers rather than -pedantic.

diff --git a/gcc/cp/decl.c b/gcc/cp/decl.c
index 420c7f40..a8cb358 100644
--- a/gcc/cp/decl.c
+++ b/gcc/cp/decl.c
@@ -1213,14 +1213,19 @@ check_redeclaration_exception_specification (tree new_decl,
      all declarations, including the definition and an explicit
      specialization, of that function shall have an
      exception-specification with the same set of type-ids.  */
-  if ((pedantic || ! DECL_IN_SYSTEM_HEADER (old_decl))
-      && ! DECL_IS_BUILTIN (old_decl)
+  if (! DECL_IS_BUILTIN (old_decl)
       && flag_exceptions
       && !comp_except_specs (new_exceptions, old_exceptions, ce_normal))
     {
-      error ("declaration of %q+F has a different exception specifier",
-	     new_decl);
-      inform (0, "from previous declaration %q+F", old_decl);
+      const char *msg
+	= "declaration of %q+F has a different exception specifier";
+      bool complained = true;
+      if (! DECL_IN_SYSTEM_HEADER (old_decl))
+	error (msg, new_decl);
+      else
+	complained = pedwarn (0, OPT_Wsystem_headers, msg, new_decl);
+      if (complained)
+	inform (0, "from previous declaration %q+F", old_decl);
     }
 }
 
diff --git a/gcc/testsuite/g++.dg/warn/Wsystem-headers1.C b/gcc/testsuite/g++.dg/warn/Wsystem-headers1.C
new file mode 100644
index 0000000..ac5c30d
--- /dev/null
+++ b/gcc/testsuite/g++.dg/warn/Wsystem-headers1.C
@@ -0,0 +1,3 @@
+#include <stdlib.h>
+
+extern double atof (const char *);
diff --git a/gcc/testsuite/g++.dg/warn/Wsystem-headers1a.C b/gcc/testsuite/g++.dg/warn/Wsystem-headers1a.C
new file mode 100644
index 0000000..68f6ea1
--- /dev/null
+++ b/gcc/testsuite/g++.dg/warn/Wsystem-headers1a.C
@@ -0,0 +1,6 @@
+// { dg-do compile { target *-*-*gnu } }
+// { dg-options "-Wsystem-headers" }
+
+#include <stdlib.h>
+
+extern double atof (const char *); // { dg-warning "different exception spec" }

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