Attachment #210584 for bug #243237

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# $FreeBSD$

PORTNAME=	mrbayes
PORTVERSION=	3.2.7a
PORTREVISION=	3
CATEGORIES=	biology
MASTER_SITES=	https://github.com/NBISweden/MrBayes/releases/download/v${PORTVERSION}/

MAINTAINER=	mzaki@e-mail.ne.jp
COMMENT=	Bayesian inference of phylogeny

LICENSE=	GPLv3
LICENSE_FILE=	${WRKSRC}/COPYING

USES=		readline:port

GNU_CONFIGURE=	yes

OPTIONS_DEFINE=		DOCS EXAMPLES

OPTIONS_DEFINE_i386=	SSE AVX FMA
OPTIONS_DEFINE_amd64=	SSE AVX FMA
OPTIONS_DEFAULT_amd64=	SSE
SSE_CONFIGURE_OFF=	--disable-sse
AVX_DESC=		Use AVX optimized routines
AVX_IMPLIES=		SSE
AVX_CONFIGURE_OFF=	--disable-avx
FMA_DESC=		Use FMA optimized routines
FMA_IMPLIES=		SSE AVX
FMA_CONFIGURE_OFF=	--disable-fma

OPTIONS_RADIO=		MPI
OPTIONS_RADIO_MPI=	MPICH OPENMPI
MPICH_LIB_DEPENDS=	libmpich.so:net/mpich
MPICH_CONFIGURE_ON=	--with-mpi
MPICH_CONFIGURE_ENV=	CC="${LOCALBASE}/bin/mpicc"
OPENMPI_LIB_DEPENDS=	libmpi.so:net/openmpi
OPENMPI_CONFIGURE_ON=	--with-mpi
OPENMPI_CONFIGURE_ENV=	CC="${LOCALBASE}/mpi/openmpi/bin/mpicc"

OPTIONS_EXCLUDE_i386=	OPENMPI

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)distinfo (-2 / +3 lines)
1	SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4	1	TIMESTAMP = 1578551242
2	SIZE (mrbayes-3.1.2.tar.gz) = 545968	2	SHA256 (mrbayes-3.2.7a.tar.gz) = 1a4670be84e6b968d59382328294db4c8ceb73e0c19c702265deec6f2177815c
		3	SIZE (mrbayes-3.2.7a.tar.gz) = 9787401




--- Makefile.orig	2005-12-22 11:13:06.000000000 -0500
+++ Makefile	2014-08-15 12:36:02.000000000 -0400
@@ -19,7 +19,7 @@
 
 # set compiler for the non-MPI version (mpicc will be used for the MPI
 # version regardless of this setting)
-CC = gcc
+CC ?= gcc
 
 # set to yes if you want to use the readline library (make sure you have it
 # installed on your machine)
@@ -67,7 +67,7 @@
 
 LIBS     +=   -lm
 
-LDFLAGS  =   $(CFLAGS)
+LDFLAGS  +=   $(CFLAGS)
 LDLIBS   =   $(LIBS)
 
 OBJECTS   =   bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o

Lines 8-11 Link Here

(-)pkg-descr (-1 / +1 lines)
8	technique called Markov chain Monte Carlo (or MCMC) to approximate the	8	technique called Markov chain Monte Carlo (or MCMC) to approximate the
9	posterior probabilities of trees.	9	posterior probabilities of trees.
10		10
11	WWW: http://mrbayes.csit.fsu.edu/	11	WWW: http://nbisweden.github.io/MrBayes/




bin/mb
%%PORTDOCS%%%%DOCSDIR%%/COPYING
%%PORTDOCS%%%%DOCSDIR%%/MBDating.pdf
%%PORTDOCS%%%%DOCSDIR%%/Manual_MrBayes_v3.2.pdf
%%PORTDOCS%%%%DOCSDIR%%/NEWS
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/hym.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/avian_ovomucoids.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codon.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cynmix.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/finch.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hymfossil.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/primates.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/replicase.nex
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sceloporus.nex

Return to bug 243237

Lines 2-31 Link Here

(-)Makefile (-16 / +28 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= mrbayes	4	PORTNAME= mrbayes
5	PORTVERSION= 3.1.2	5	PORTVERSION= 3.2.7a
6	PORTREVISION= 3
7	CATEGORIES= biology	6	CATEGORIES= biology
8	MASTER_SITES= SF	7	MASTER_SITES= https://github.com/NBISweden/MrBayes/releases/download/v${PORTVERSION}/
9		8
10	MAINTAINER= mzaki@m.u-tokyo.ac.jp	9	MAINTAINER= mzaki@e-mail.ne.jp
11	COMMENT= Bayesian inference of phylogeny	10	COMMENT= Bayesian inference of phylogeny
12		11
13	BROKEN= unfetchable	12	LICENSE= GPLv3
		13	LICENSE_FILE= ${WRKSRC}/COPYING
14		14
15	OPTIONS_DEFINE= EXAMPLES	15	USES= readline:port
16		16
17	USES= gmake readline:port	17	GNU_CONFIGURE= yes
18		18
19	PLIST_FILES= bin/mb	19	OPTIONS_DEFINE= DOCS EXAMPLES
20		20
21	PORTEXAMPLES= adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \	21	OPTIONS_DEFINE_i386= SSE AVX FMA
22	cynmix.nex kim.nex primates.nex replicase.nex	22	OPTIONS_DEFINE_amd64= SSE AVX FMA
		23	OPTIONS_DEFAULT_amd64= SSE
		24	SSE_CONFIGURE_OFF= --disable-sse
		25	AVX_DESC= Use AVX optimized routines
		26	AVX_IMPLIES= SSE
		27	AVX_CONFIGURE_OFF= --disable-avx
		28	FMA_DESC= Use FMA optimized routines
		29	FMA_IMPLIES= SSE AVX
		30	FMA_CONFIGURE_OFF= --disable-fma
23		31
24	do-install:	32	OPTIONS_RADIO= MPI
25	${INSTALL_PROGRAM} ${WRKSRC}/mb ${STAGEDIR}${PREFIX}/bin/	33	OPTIONS_RADIO_MPI= MPICH OPENMPI
26	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}	34	MPICH_LIB_DEPENDS= libmpich.so:net/mpich
27	.for file in ${PORTEXAMPLES}	35	MPICH_CONFIGURE_ON= --with-mpi
28	${INSTALL_DATA} ${WRKSRC}/${file} ${STAGEDIR}${EXAMPLESDIR}	36	MPICH_CONFIGURE_ENV= CC="${LOCALBASE}/bin/mpicc"
29	.endfor	37	OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi
		38	OPENMPI_CONFIGURE_ON= --with-mpi
		39	OPENMPI_CONFIGURE_ENV= CC="${LOCALBASE}/mpi/openmpi/bin/mpicc"
30		40
		41	OPTIONS_EXCLUDE_i386= OPENMPI
		42
31	.include <bsd.port.mk>	43	.include <bsd.port.mk>

Lines 1-20 Link Here

(-)files/patch-Makefile (-20 lines)
1	--- Makefile.orig 2005-12-22 11:13:06.000000000 -0500
2	+++ Makefile 2014-08-15 12:36:02.000000000 -0400
3	@@ -19,7 +19,7 @@
4
5	# set compiler for the non-MPI version (mpicc will be used for the MPI
6	# version regardless of this setting)
7	-CC = gcc
8	+CC ?= gcc
9
10	# set to yes if you want to use the readline library (make sure you have it
11	# installed on your machine)
12	@@ -67,7 +67,7 @@
13
14	LIBS += -lm
15
16	-LDFLAGS = $(CFLAGS)
17	+LDFLAGS += $(CFLAGS)
18	LDLIBS = $(LIBS)
19
20	OBJECTS = bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o

Line 0 Link Here

(-)pkg-plist (+15 lines)
	1	bin/mb
	2	%%PORTDOCS%%%%DOCSDIR%%/COPYING
	3	%%PORTDOCS%%%%DOCSDIR%%/MBDating.pdf
	4	%%PORTDOCS%%%%DOCSDIR%%/Manual_MrBayes_v3.2.pdf
	5	%%PORTDOCS%%%%DOCSDIR%%/NEWS
	6	%%PORTDOCS%%%%DOCSDIR%%/README
	7	%%PORTDOCS%%%%DOCSDIR%%/hym.nex
	8	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/avian_ovomucoids.nex
	9	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/codon.nex
	10	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cynmix.nex
	11	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/finch.nex
	12	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hymfossil.nex
	13	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/primates.nex
	14	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/replicase.nex
	15	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sceloporus.nex