ports/184857: biology/grappa: Support CFLAGS properly

[KATO Tsuguru]

>Number:         184857
>Category:       ports
>Synopsis:       biology/grappa: Support CFLAGS properly
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Dec 16 18:10:15 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p4 i386
>Organization:
>Environment:
>Description:
- Support CFLAGS properly

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/grappa/Makefile biology/grappa/Makefile
--- /usr/ports/biology/grappa/Makefile	2013-12-11 05:39:55.000000000 +0900
+++ biology/grappa/Makefile	2013-12-17 00:00:00.000000000 +0900
@@ -3,6 +3,7 @@
 
 PORTNAME=	grappa
 PORTVERSION=	2.0
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://www.cs.unm.edu/~moret/GRAPPA/
 DISTNAME=	GRAPPA20
@@ -10,14 +11,13 @@
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	Genome Rearrangements Analysis and Phylogeny Software
 
-USES=	gmake
-MAKE_ARGS=	CC="${CC}"
+USES=		gmake
 
 PLIST_FILES=	bin/grappa bin/invdist bin/distmat
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/grappa ${STAGEDIR}${PREFIX}/bin
-	${LN} -sf ${PREFIX}/bin/grappa ${STAGEDIR}${PREFIX}/bin/invdist
-	${LN} -sf ${PREFIX}/bin/grappa ${STAGEDIR}${PREFIX}/bin/distmat
+	(cd ${WRKSRC} && ${INSTALL_PROGRAM} grappa ${STAGEDIR}${PREFIX}/bin)
+	${LN} -sf grappa ${STAGEDIR}${PREFIX}/bin/invdist
+	${LN} -sf grappa ${STAGEDIR}${PREFIX}/bin/distmat
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/grappa/files/patch-Makefile biology/grappa/files/patch-Makefile
--- /usr/ports/biology/grappa/files/patch-Makefile	2013-11-06 22:05:43.000000000 +0900
+++ biology/grappa/files/patch-Makefile	2013-12-17 00:00:00.000000000 +0900
@@ -1,6 +1,42 @@
 --- Makefile.orig	2004-09-22 09:09:18.000000000 -0500
 +++ Makefile	2011-03-26 13:49:31.000000000 -0500
-@@ -156,8 +156,2 @@
+@@ -47,7 +47,7 @@
+ endif
+ 
+ # GNU C
+-CC = gcc 
++CC ?= gcc 
+ 
+ # Microsoft C
+ # CC = cl
+@@ -62,13 +62,13 @@
+ #CC = tmcc -DMPBPA
+ 
+ # Default CFLAGS
+-CFLAGS := -D${OS} $(CONCORDE_CFLAGS) $(GMP_CFLAGS) -DINIT 
++CFLAGS += -D${OS} $(CONCORDE_CFLAGS) $(GMP_CFLAGS) -DINIT 
+ 
+ # TESTING option for CFLAGS
+ # CFLAGS := -DTESTING $(CFLAGS)
+ 
+ ifeq ($(strip $(CC)), gcc)
+-CFLAGS := -O3 -Wall -DGCC $(CFLAGS)
++CFLAGS := -Wall -DGCC $(CFLAGS)
+ endif
+ ifeq ($(strip $(CC)), pgcc)
+ CFLAGS := -fast $(CFLAGS)
+@@ -115,7 +115,7 @@
+ RELBASE   = GRAPPA
+ RELNAME   = $(RELBASE)-$(VERS_MAJ).$(VERS_MIN)
+ 
+-LIBS 		:= -lm -lc -lpthread 
++LIBS 		:= -lm -pthread 
+ # added this part to the end of above "-l mpi"
+ ifeq ($(OS), SunOS)
+ LIBS		:= -liberty -lsocket -lposix4 -lnsl ${LIBS}
+@@ -154,12 +154,6 @@
+ 	$(RM) -fr $(RELNAME)
+ 	$(LS) -l $(RELNAME).tar.gz
  
 -$(RELNAME)/%.c : %.c
 -	-$(CP) $< $(RELNAME)/.
@@ -9,3 +45,5 @@
 -	-$(CP) $< $(RELNAME)/.
 -
  clean:
+ 	-rm -f *.${OBJ_SUFFIX} *~ ${EXEC} ${EXEC}.${EXE_SUFFIX} ${SYM} \
+ 	       core gmon.out
>Release-Note:
>Audit-Trail:
>Unformatted: