diff --git a/cmake/Scripts/DuneCompat2.cmake b/cmake/Scripts/DuneCompat2.cmake
index e6a83258..86780776 100644
--- a/cmake/Scripts/DuneCompat2.cmake
+++ b/cmake/Scripts/DuneCompat2.cmake
@@ -5,12 +5,19 @@ set (base_dir ".")
 set (marker_file "${base_dir}/CMakeFiles/marker")
 set (makefile "${base_dir}/Makefile")
 
-# if the Makefile has changed, then update it and touch the marker so that
-# the marker is newer and won't update the Makefile again
+# if the Makefile has changed, then update it
 if ("${makefile}" IS_NEWER_THAN "${marker_file}")
-  file (APPEND "${makefile}"
-	"abs_top_srcdir = ${CMAKE_HOME_DIRECTORY}\n"
+  # only add the string once, so it does not return multiple
+  # results for the command line (will lead to syntax error)
+  file (STRINGS "${makefile}" abs_top_srcdir_FOUND
+	REGEX "^abs_top_srcdir = "
 	)
+  if (NOT abs_top_srcdir_FOUND)
+	file (APPEND "${makefile}"
+	  "abs_top_srcdir = ${CMAKE_HOME_DIRECTORY}\n"
+	  )
+  endif (NOT abs_top_srcdir_FOUND)
+  # touch the marker so that we won't update the Makefile again
   execute_process (COMMAND
 	${CMAKE_COMMAND} -E touch "${marker_file}"
 	)