gentoo-overlay/sci-biology/poa/files/poa-2-respect-flags.patch

--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,3 @@
-
-AR=ar rc
-
 TARGETS=poa liblpo.a poa_doc libbflag.a
 
 # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS
@@ -26,9 +23,8 @@
 	stringptr.o
 
 
-CC = gcc
 #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
+CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
 # -I$(HOME)/lib/include
 # -DREPORT_MAX_ALLOC
 
@@ -37,14 +33,14 @@
 
 liblpo.a: $(LIBOBJECTS)
 	rm -f $@
-	$(AR) $@ $(LIBOBJECTS)
-	ranlib $@
+	$(AR) rc $@ $(LIBOBJECTS)
+	$(RANLIB) $@
 
 
 
 # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
 poa: $(OBJECTS) liblpo.a
-	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
 
 what:
 	@echo poa: partial-order based sequence alignment program