some patches to compile on linux

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@205 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/Makefile

@@ -6,7 +6,7 @@ PRIMER_OBJ= $(patsubst %.c,%.o,$(PRIMER_SRC))
 
 SRCS= $(PRIMER_SRC) 
 
-LIB= -lecoPCR -lecoprimer -lz -lm
+LIB= -lecoprimer -lecoPCR -lz -lm
 
 LIBFILE= libecoPCR/libecoPCR.a \
          libecoprimer/libecoprimer.a
@@ -26,7 +26,7 @@ all: $(EXEC)
 # executable compilation and link
 
 ecoPrimer: $(PRIMER_OBJ) $(LIBFILE) 
-	$(CC) $(LDFLAGS) -O5 -m64 -fast -o $@ $< $(LIBPATH) $(LIB)
+	$(CC) $(LDFLAGS) -O5 -m64 -o $@ $< $(LIBPATH) $(LIB)
 	
 
 ########
@@ -55,4 +55,4 @@ clean:
 	$(MAKE) -C libecoprimer clean
 		
 
-		
+		

src/global.mk

@@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
 MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
 
 CC=gcc
-CFLAGS= -W -Wall -O5 -m64 -fast -g
+CFLAGS= -W -Wall -O5 -m64 
 #CFLAGS= -W -Wall -O0 -m64  -g
 #CFLAGS= -W -Wall -O5 -fast -g
 
@@ -17,4 +17,4 @@ default: all
 	@sed 's/\($*\)\.o[ :]*/\1.o $@ : /g' < $*.d > $@; \
 	rm -f $*.d; [ -s $@ ] || rm -f $@
 
-include $(SRCS:.c=.P)
+include $(SRCS:.c=.P)

src/libecoPCR/ecofilter.c

@@ -16,4 +16,5 @@ int eco_is_taxid_included(	ecotaxonomy_t *taxonomy,
 			return 1;
 	
 	return 0;
-}
+}
+

src/libecoprimer/aproxpattern.c

@@ -39,8 +39,8 @@ ppattern_t buildPatternFromWord(word_t word, uint32_t patlen)
 }
 
 
-#ifdef IS_UPPER(c)
-#undef IS_UPPER(c)
+#ifdef IS_UPPER
+#undef IS_UPPER
 #endif
 
 /* -------------------------------------------- */