https://github.com/abacus-gene/paml/pull/46
--- a/src/Makefile
+++ b/src/Makefile
@@ -9,39 +9,39 @@ LIBS = -lm # -lM
 all : $(PRGS)
 
 baseml : baseml.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ baseml.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.o tools.o $(LIBS)
 basemlg : basemlg.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ basemlg.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.o tools.o $(LIBS)
 codeml : codeml.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ codeml.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.o tools.o $(LIBS)
 evolver : evolver.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ evolver.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.o tools.o $(LIBS)
 pamp : pamp.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ pamp.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.o tools.o $(LIBS)
 mcmctree : mcmctree.o tools.o treesub.c treespace.c paml.h
-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
 yn00: yn00.o tools.o paml.h
-	$(CC) $(CFLAGS) -o $@ yn00.o tools.o $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.o tools.o $(LIBS)
 chi2 : chi2.o
-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
+	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
 
 tools.o : paml.h tools.c
-	$(CC) $(CFLAGS) -c tools.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c tools.c
 baseml.o : paml.h baseml.c treesub.c treespace.c
-	$(CC) $(CFLAGS) -c baseml.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c baseml.c
 basemlg.o : paml.h basemlg.c treesub.c
-	$(CC) $(CFLAGS) -c basemlg.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c basemlg.c
 codeml.o : paml.h codeml.c treesub.c treespace.c
-	$(CC) $(CFLAGS) -c codeml.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c codeml.c
 evolver.o: evolver.c treesub.c treespace.c
-	$(CC) $(CFLAGS) -c evolver.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c evolver.c
 mcmctree.o : paml.h mcmctree.c treesub.c treespace.c
-	$(CC) $(CFLAGS) -c mcmctree.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c mcmctree.c
 pamp.o : paml.h pamp.c treesub.c treespace.c
-	$(CC) $(CFLAGS) -c pamp.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c pamp.c
 yn00.o : paml.h yn00.c
-	$(CC) $(CFLAGS) -c yn00.c
+	$(CC) $(CPPFLAGS) $(CFLAGS) -c yn00.c
 
 clean :
 	-rm *.o $(PRGS)