Index: include/clang/Driver/Options.td
===================================================================
--- include/clang/Driver/Options.td
+++ include/clang/Driver/Options.td
@@ -1969,7 +1969,8 @@
 def _all_warnings : Flag<["--"], "all-warnings">, Alias<Wall>;
 def _analyze_auto : Flag<["--"], "analyze-auto">, Flags<[DriverOption]>;
 def _analyzer_no_default_checks : Flag<["--"], "analyzer-no-default-checks">, Flags<[DriverOption]>;
-def _analyzer_output : JoinedOrSeparate<["--"], "analyzer-output">, Flags<[DriverOption]>;
+def _analyzer_output : JoinedOrSeparate<["--"], "analyzer-output">, Flags<[DriverOption]>,
+  HelpText<"Static analyzer report output format (html|plist|plist-multi-file|plist-html|text).">;
 def _analyze : Flag<["--"], "analyze">, Flags<[DriverOption, CoreOption]>,
   HelpText<"Run the static analyzer">;
 def _assemble : Flag<["--"], "assemble">, Alias<S>;
Index: lib/StaticAnalyzer/Core/PathDiagnostic.cpp
===================================================================
--- lib/StaticAnalyzer/Core/PathDiagnostic.cpp
+++ lib/StaticAnalyzer/Core/PathDiagnostic.cpp
@@ -211,6 +211,12 @@
     const SourceManager &SMgr = D->path.front()->getLocation().getManager();
     SmallVector<const PathPieces *, 5> WorkList;
     WorkList.push_back(&D->path);
+    SmallString<128> buf;
+    llvm::raw_svector_ostream warning(buf);
+    warning << "warning: Path diagnostic report is not generated. Current "
+            << "output format does not support diagnostics that cross file "
+            << "boundaries. Refer to --analyzer-output for valid output "
+            << "formats\n";
 
     while (!WorkList.empty()) {
       const PathPieces &path = *WorkList.pop_back_val();
@@ -222,19 +228,25 @@
 
         if (FID.isInvalid()) {
           FID = SMgr.getFileID(L);
-        } else if (SMgr.getFileID(L) != FID)
-          return; // FIXME: Emit a warning?
+        } else if (SMgr.getFileID(L) != FID) {
+          llvm::errs() << warning.str();
+          return;
+        }
 
         // Check the source ranges.
         ArrayRef<SourceRange> Ranges = piece->getRanges();
         for (ArrayRef<SourceRange>::iterator I = Ranges.begin(),
                                              E = Ranges.end(); I != E; ++I) {
           SourceLocation L = SMgr.getExpansionLoc(I->getBegin());
-          if (!L.isFileID() || SMgr.getFileID(L) != FID)
-            return; // FIXME: Emit a warning?
+          if (!L.isFileID() || SMgr.getFileID(L) != FID) {
+            llvm::errs() << warning.str();
+            return;
+          }
           L = SMgr.getExpansionLoc(I->getEnd());
-          if (!L.isFileID() || SMgr.getFileID(L) != FID)
-            return; // FIXME: Emit a warning?
+          if (!L.isFileID() || SMgr.getFileID(L) != FID) {
+            llvm::errs() << warning.str();
+            return;
+          }
         }
 
         if (const PathDiagnosticCallPiece *call =
Index: test/Analysis/diagnostics/diag-cross-file-boundaries.h
===================================================================
--- test/Analysis/diagnostics/diag-cross-file-boundaries.h
+++ test/Analysis/diagnostics/diag-cross-file-boundaries.h
@@ -0,0 +1,4 @@
+static void f() {
+  int *p = 0;
+  *p = 1;       // expected-warning{{Dereference of null pointer}}
+}
Index: test/Analysis/diagnostics/diag-cross-file-boundaries.c
===================================================================
--- test/Analysis/diagnostics/diag-cross-file-boundaries.c
+++ test/Analysis/diagnostics/diag-cross-file-boundaries.c
@@ -0,0 +1,12 @@
+// RUN: %clang_cc1 -analyze -analyzer-checker=core -verify %s
+// RUN: %clang_cc1 -analyze -analyzer-checker=core -analyzer-output=html -o PR12421.html %s 2>&1 | FileCheck %s
+
+// Test for PR12421
+#include "diag-cross-file-boundaries.h"
+
+int main(){
+  f();
+  return 0;
+}
+
+// CHECK: warning: Path diagnostic report is not generated.