Attachment 210584 Details for Bug 243237 – svn diff for biology/mrbayes to 3.2.7a

[patch] svn diff for biology/mrbayes to 3.2.7a

mrbayes-3.2.7a.diff (text/plain), 4.64 KB, created by Motomichi Matsuzaki on 2020-01-10 08:00:14 UTC

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Creator: Motomichi Matsuzaki

Created: 2020-01-10 08:00:14 UTC

Size: 4.64 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 522468)
>+++ Makefile	(working copy)
>@@ -2,30 +2,42 @@
> # $FreeBSD$
> 
> PORTNAME=	mrbayes
>-PORTVERSION=	3.1.2
>-PORTREVISION=	3
>+PORTVERSION=	3.2.7a
> CATEGORIES=	biology
>-MASTER_SITES=	SF
>+MASTER_SITES=	https://github.com/NBISweden/MrBayes/releases/download/v${PORTVERSION}/
> 
>-MAINTAINER=	mzaki@m.u-tokyo.ac.jp
>+MAINTAINER=	mzaki@e-mail.ne.jp
> COMMENT=	Bayesian inference of phylogeny
> 
>-BROKEN=		unfetchable
>+LICENSE=	GPLv3
>+LICENSE_FILE=	${WRKSRC}/COPYING
> 
>-OPTIONS_DEFINE=	EXAMPLES
>+USES=		readline:port
> 
>-USES=		gmake readline:port
>+GNU_CONFIGURE=	yes
> 
>-PLIST_FILES=	bin/mb
>+OPTIONS_DEFINE=		DOCS EXAMPLES
> 
>-PORTEXAMPLES=	adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \
>-		cynmix.nex kim.nex primates.nex replicase.nex
>+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
> 
>-do-install:
>-	${INSTALL_PROGRAM} ${WRKSRC}/mb ${STAGEDIR}${PREFIX}/bin/
>-	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
>-.for file in ${PORTEXAMPLES}
>-	${INSTALL_DATA} ${WRKSRC}/${file} ${STAGEDIR}${EXAMPLESDIR}
>-.endfor
>+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>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 522468)
>+++ distinfo	(working copy)
>@@ -1,2 +1,3 @@
>-SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4
>-SIZE (mrbayes-3.1.2.tar.gz) = 545968
>+TIMESTAMP = 1578551242
>+SHA256 (mrbayes-3.2.7a.tar.gz) = 1a4670be84e6b968d59382328294db4c8ceb73e0c19c702265deec6f2177815c
>+SIZE (mrbayes-3.2.7a.tar.gz) = 9787401
>Index: files/patch-Makefile
>===================================================================
>--- files/patch-Makefile	(revision 522468)
>+++ files/patch-Makefile	(nonexistent)
>@@ -1,20 +0,0 @@
>---- 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
>
>Property changes on: files/patch-Makefile
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(revision 522468)
>+++ pkg-descr	(working copy)
>@@ -8,4 +8,4 @@
> technique called Markov chain Monte Carlo (or MCMC) to approximate the
> posterior probabilities of trees.
> 
>-WWW: http://mrbayes.csit.fsu.edu/
>+WWW: http://nbisweden.github.io/MrBayes/
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(nonexistent)
>+++ pkg-plist	(working copy)
>@@ -0,0 +1,15 @@
>+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
>
>Property changes on: pkg-plist
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

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Attachments on bug 243237: 210584