casa-mp-base

diff -ur ../exonerate-2.2.0.orig/src/program/Makefile.am ./src/program/Makefile.am

--- ../exonerate-2.2.0.orig/src/program/Makefile.am 2008-02-08 17:35:36.000000000 +0000

+++ ./src/program/Makefile.am   2012-02-23 16:31:14.000000000 +0000

@@ -67,9 +67,9 @@

 BUILT_SOURCES = c4_model_archive.a

 BOOTSTRAPPER = $(top_srcdir)/src/model/bootstrapper

 c4_model_archive.h: $(BOOTSTRAPPER)

-   $(BOOTSTRAPPER) --compiled no

+   CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no

 c4_model_archive.a: $(BOOTSTRAPPER)

-   $(BOOTSTRAPPER) --compiled no

+   CFLAGS="$(CFLAGS)" $(BOOTSTRAPPER) --compiled no

 # Special viterbi.o and scheduler.o for compiled model linking

 viterbi.o: $(top_srcdir)/src/c4/viterbi.c