gentoo-overlay/sci-biology/paml/files/paml-4.9j-makefile.patch

--- a/src/Makefile
+++ b/src/Makefile
@@ -1,27 +1,18 @@
-PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 
-CC = cc # cc, gcc, cl
+PRGS =  baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2
 
-CFLAGS = -O3
+CFLAGS += -Wno-unused-result
 #CFLAGS = -fast
 
-LIBS = -lm # -lM
+LDLIBS = -lm
 
 all : $(PRGS)
 
-baseml : baseml.c tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
-basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
-codeml : codeml.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
-evolver : evolver.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
-pamp : pamp.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
-mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
-yn00: yn00.c tools.c paml.h
-	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
-chi2 : chi2.c
-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
+baseml: tools.o paml.h 
+basemlg: tools.o paml.h 
+codeml: tools.o paml.h 
+evolver: tools.o paml.h 
+pamp: tools.o paml.h 
+mcmctree: tools.o paml.h 
+infinitesites: tools.o paml.h 
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)
+yn00: tools.o paml.h