From owner-svn-ports-all@FreeBSD.ORG Fri Dec 20 13:27:13 2013 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id DEE16981; Fri, 20 Dec 2013 13:27:13 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id B15A9149B; Fri, 20 Dec 2013 13:27:13 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.7/8.14.7) with ESMTP id rBKDRDuv065247; Fri, 20 Dec 2013 13:27:13 GMT (envelope-from pawel@svn.freebsd.org) Received: (from pawel@localhost) by svn.freebsd.org (8.14.7/8.14.7/Submit) id rBKDRDei065245; Fri, 20 Dec 2013 13:27:13 GMT (envelope-from pawel@svn.freebsd.org) Message-Id: <201312201327.rBKDRDei065245@svn.freebsd.org> From: Pawel Pekala Date: Fri, 20 Dec 2013 13:27:13 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r337010 - in head/biology/grappa: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 20 Dec 2013 13:27:13 -0000 Author: pawel Date: Fri Dec 20 13:27:13 2013 New Revision: 337010 URL: http://svnweb.freebsd.org/changeset/ports/337010 Log: - Respect CC/CFLAGS PR: ports/184857 Submitted by: KATO Tsuguru Modified: head/biology/grappa/Makefile (contents, props changed) head/biology/grappa/files/patch-Makefile (contents, props changed) Modified: head/biology/grappa/Makefile ============================================================================== --- head/biology/grappa/Makefile Fri Dec 20 13:16:21 2013 (r337009) +++ head/biology/grappa/Makefile Fri Dec 20 13:27:13 2013 (r337010) @@ -10,14 +10,13 @@ DISTNAME= GRAPPA20 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 Modified: head/biology/grappa/files/patch-Makefile ============================================================================== --- head/biology/grappa/files/patch-Makefile Fri Dec 20 13:16:21 2013 (r337009) +++ head/biology/grappa/files/patch-Makefile Fri Dec 20 13:27:13 2013 (r337010) @@ -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