diff -r 9a7d81d66d09 -r d55eb82ae77b src/Pure/System/options.scala
--- a/src/Pure/System/options.scala	Mon Jan 14 21:37:42 2013 +0100
+++ b/src/Pure/System/options.scala	Mon Jan 14 22:24:57 2013 +0100
@@ -348,7 +348,7 @@
       changed.sortBy(_._1)
         .map({ case (x, y, z) => x + " = " + Outer_Syntax.quote_string(y) + z + "\n" }).mkString
 
-    Options.PREFS_DIR.file.mkdirs()
+    Isabelle_System.mkdirs(Options.PREFS_DIR)
     Options.PREFS.file renameTo Options.PREFS_BACKUP.file
     File.write(Options.PREFS,
       "(* generated by Isabelle " + Calendar.getInstance.getTime + " *)\n\n" + prefs)