Attachment 138774 Details for Bug 184857 – file.diff

[patch] file.diff

file.diff (text/plain), 2.41 KB, created by tkato432 on 2013-12-16 18:10:15 UTC

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Creator: tkato432

Created: 2013-12-16 18:10:15 UTC

Size: 2.41 KB

patch

obsolete

>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@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

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