You cannot have two modules which both redefine the output format. This is a stupid patch. Something more clever might be done in the c++ code.

--
Julien
Index: lib/layouts/sweave.module
===================================================================
--- lib/layouts/sweave.module   (revision 37999)
+++ lib/layouts/sweave.module   (working copy)
@@ -4,6 +4,7 @@
 #See sweave.lyx in examples.
 #DescriptionEnd
 #Category: literate
+#Excludes: lilypond
 
 
 # To add :
Index: lib/layouts/lilypond.module
===================================================================
--- lib/layouts/lilypond.module (revision 37999)
+++ lib/layouts/lilypond.module (working copy)
@@ -3,6 +3,7 @@
 #This module adds an inset to enter LilyPond code directly into LyX.
 #It will be processed in the output. See the lilypond.lyx example file.
 #DescriptionEnd
+#Excludes: sweave
 
 # Author: Julien Rioux <jri...@physics.utoronto.ca>
 

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