Attachment #43423 for bug #67429

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#

PORTNAME=	migrate
PORTVERSION=	1.7.6.1
CATEGORIES=	biology
MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/
DISTNAME=	${PORTNAME}-${PORTVERSION}.src

MAINTAINER=	wjv@FreeBSD.org
COMMENT=	A program to estimate population sizes and migration rates

WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
CONFIGURE_WRKSRC=	${WRKSRC}/src
BUILD_WRKSRC=	${CONFIGURE_WRKSRC}
INSTALL_WRKSRC=	${CONFIGURE_WRKSRC}
GNU_CONFIGURE=	yes
CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}

MAN1=		migrate.1
MLINKS=		migrate.1 migrate-n.1

DOCS=		HISTORY HOWTO-PARALLEL README migrate.html
EXAMPLES=	README infile.benchmark infile.ep infile.msat infile.seq \
		parmfile parmfile.benchmark parmfile.ep parmfile.msat \
		parmfile.seq

do-install:
	@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
	@ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate
	@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
.if !defined(NOPORTDOCS)
	@ ${MKDIR} ${DOCSDIR}/graphics
.for file in ${DOCS}
	@ ${INSTALL_DATA} ${WRKSRC}/../${file} ${DOCSDIR}
.endfor
	@ ${MKDIR} ${EXAMPLESDIR}
.for file in ${EXAMPLES}
	@ ${INSTALL_DATA} ${WRKSRC}/../example/${file} ${EXAMPLESDIR}
.endfor
	@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
.endif

.include <bsd.port.pre.mk>

Lines 1-2 Link Here

(-)biology/migrate/distinfo (-2 / +2 lines)
1	MD5 (migrate-1.2.4.src.tar.gz) = d5b90497336bee7d559ac3a654043e13	1	MD5 (migrate-1.7.6.1.src.tar.gz) = 5e8f03923ca2a12e7d3dd460c17679a1
2	SIZE (migrate-1.2.4.src.tar.gz) = 312245	2	SIZE (migrate-1.7.6.1.src.tar.gz) = 384925




%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
%%PORTDOCS%%%%DOCSDIR%%/migrate.html
%%PORTDOCS%%%%EXAMPLESDIR%%/README
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.benchmark
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat
%%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.benchmark
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.ep
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.msat
%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.seq
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
%%PORTDOCS%%@dirrm %%DOCSDIR%%

Added Link Here

(-)biology/migrate/files/patch-Makefile.in (+11 lines)
1	--- Makefile.in.orig Mon May 10 15:58:32 2004
2	+++ Makefile.in Tue Jun 1 01:44:25 2004
3	@@ -39,7 +39,7 @@
4	COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DNEWSTYLE
5	#COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DNEWSTYLE -DMERSENNE_TWISTER
6	COMMONVFLAGS = $(COMMONFLAGS)
7	-CFLAGS = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
8	+CFLAGS += @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
9	# IBM PowerPC compiler on macosx needs also CC=xlc
10	#CFLAGS = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded -Dpowerpc $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\" $(MIGRATEVERSION)\\\"\"
11	THREADCFLAGS= @THREADCFLAGS@

Return to bug 67429

Lines 6-12 Link Here

(-)biology/migrate/Makefile (-9 / +19 lines)
6	#	6	#
7		7
8	PORTNAME= migrate	8	PORTNAME= migrate
9	PORTVERSION= 1.2.4	9	PORTVERSION= 1.7.6.1
10	CATEGORIES= biology	10	CATEGORIES= biology
11	MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/	11	MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/lamarc/migrate/
12	DISTNAME= ${PORTNAME}-${PORTVERSION}.src	12	DISTNAME= ${PORTNAME}-${PORTVERSION}.src
Lines 14-35 Link Here
14	MAINTAINER= wjv@FreeBSD.org	14	MAINTAINER= wjv@FreeBSD.org
15	COMMENT= A program to estimate population sizes and migration rates	15	COMMENT= A program to estimate population sizes and migration rates
16		16
17	WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}	17	WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
18	CONFIGURE_WRKSRC= ${WRKSRC}/src
19	BUILD_WRKSRC= ${CONFIGURE_WRKSRC}
20	INSTALL_WRKSRC= ${CONFIGURE_WRKSRC}
21	GNU_CONFIGURE= yes	18	GNU_CONFIGURE= yes
		19	CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
22		20
23	MAN1= migrate.1	21	MAN1= migrate.1
		22	MLINKS= migrate.1 migrate-n.1
24		23
25	post-install:	24	DOCS= HISTORY HOWTO-PARALLEL README migrate.html
		25	EXAMPLES= README infile.benchmark infile.ep infile.msat infile.seq \
		26	parmfile parmfile.benchmark parmfile.ep parmfile.msat \
		27	parmfile.seq
		28
		29	do-install:
		30	@ ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin
26	@ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate	31	@ cd ${PREFIX}/bin && ${LN} -s migrate-n migrate
		32	@ ${INSTALL_MAN} ${WRKSRC}/migrate.1 ${MAN1PREFIX}/man/man1
27	.if !defined(NOPORTDOCS)	33	.if !defined(NOPORTDOCS)
28	@ ${MKDIR} ${DOCSDIR}/graphics	34	@ ${MKDIR} ${DOCSDIR}/graphics
29	.for docfile in HISTORY HOWTO-PARALLEL README migrate.html	35	.for file in ${DOCS}
30	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}	36	@ ${INSTALL_DATA} ${WRKSRC}/../${file} ${DOCSDIR}
		37	.endfor
		38	@ ${MKDIR} ${EXAMPLESDIR}
		39	.for file in ${EXAMPLES}
		40	@ ${INSTALL_DATA} ${WRKSRC}/../example/${file} ${EXAMPLESDIR}
31	.endfor	41	.endfor
32	@ ${INSTALL_DATA} ${WRKSRC}/graphics/* ${DOCSDIR}/graphics	42	@ ${INSTALL_DATA} ${WRKSRC}/../graphics/* ${DOCSDIR}/graphics
33	.endif	43	.endif
34		44
35	.include <bsd.port.pre.mk>	45	.include <bsd.port.pre.mk>

Lines 8-12 Link Here

(-)biology/migrate/pkg-plist (+11 lines)
8	%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif	8	%%PORTDOCS%%%%DOCSDIR%%/graphics/migrate.gif
9	%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif	9	%%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif
10	%%PORTDOCS%%%%DOCSDIR%%/migrate.html	10	%%PORTDOCS%%%%DOCSDIR%%/migrate.html
		11	%%PORTDOCS%%%%EXAMPLESDIR%%/README
		12	%%PORTDOCS%%%%EXAMPLESDIR%%/infile.benchmark
		13	%%PORTDOCS%%%%EXAMPLESDIR%%/infile.ep
		14	%%PORTDOCS%%%%EXAMPLESDIR%%/infile.msat
		15	%%PORTDOCS%%%%EXAMPLESDIR%%/infile.seq
		16	%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile
		17	%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.benchmark
		18	%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.ep
		19	%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.msat
		20	%%PORTDOCS%%%%EXAMPLESDIR%%/parmfile.seq
		21	%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
11	%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics	22	%%PORTDOCS%%@dirrm %%DOCSDIR%%/graphics
12	%%PORTDOCS%%@dirrm %%DOCSDIR%%	23	%%PORTDOCS%%@dirrm %%DOCSDIR%%