Date: Sat, 29 Feb 2020 23:24:40 +0000 (UTC) From: Joseph Mingrone <jrm@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r527483 - in head/biology/mrbayes: . files Message-ID: <202002292324.01TNOeWK021507@repo.freebsd.org>
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Author: jrm Date: Sat Feb 29 23:24:39 2020 New Revision: 527483 URL: https://svnweb.freebsd.org/changeset/ports/527483 Log: biology/mrbayes: Update to version 3.2.7 PR: 243237 Submitted by: mzaki@e-mail.ne.jp (maintainer, with modifications) Added: head/biology/mrbayes/pkg-message (contents, props changed) head/biology/mrbayes/pkg-plist (contents, props changed) Deleted: head/biology/mrbayes/files/ Modified: head/biology/mrbayes/Makefile (contents, props changed) head/biology/mrbayes/distinfo (contents, props changed) head/biology/mrbayes/pkg-descr (contents, props changed) Modified: head/biology/mrbayes/Makefile ============================================================================== --- head/biology/mrbayes/Makefile Sat Feb 29 23:05:34 2020 (r527482) +++ head/biology/mrbayes/Makefile Sat Feb 29 23:24:39 2020 (r527483) @@ -2,30 +2,47 @@ # $FreeBSD$ PORTNAME= mrbayes -PORTVERSION= 3.1.2 -PORTREVISION= 3 +DISTVERSIONPREFIX= v +DISTVERSION= 3.2.7 CATEGORIES= biology -MASTER_SITES= SF -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 +USE_GITHUB= yes +GH_ACCOUNT= NBISweden +GH_PROJECT= MrBayes -USES= gmake readline:port +GNU_CONFIGURE= yes -PLIST_FILES= bin/mb +OPTIONS_DEFINE= DOCS EXAMPLES +OPTIONS_DEFINE_amd64= AVX FMA SSE +OPTIONS_DEFINE_i386= AVX FMA SSE -PORTEXAMPLES= adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \ - cynmix.nex kim.nex primates.nex replicase.nex +OPTIONS_DEFAULT_amd64= SSE -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 + +OPTIONS_EXCLUDE_i386= OPENMPI + +AVX_DESC= Use AVX optimized routines +FMA_DESC= Use FMA optimized routines + +AVX_IMPLIES= SSE +AVX_CONFIGURE_OFF= --disable-avx +FMA_IMPLIES= AVX SSE +FMA_CONFIGURE_OFF= --disable-fma +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" +SSE_CONFIGURE_OFF= --disable-sse .include <bsd.port.mk> Modified: head/biology/mrbayes/distinfo ============================================================================== --- head/biology/mrbayes/distinfo Sat Feb 29 23:05:34 2020 (r527482) +++ head/biology/mrbayes/distinfo Sat Feb 29 23:24:39 2020 (r527483) @@ -1,2 +1,3 @@ -SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 -SIZE (mrbayes-3.1.2.tar.gz) = 545968 +TIMESTAMP = 1583009863 +SHA256 (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 64da39c01f606d0413ce90a1dd3c1ce2cbdef4cbad99aee8a4b2391a2e8db244 +SIZE (NBISweden-MrBayes-v3.2.7_GH0.tar.gz) = 9825172 Modified: head/biology/mrbayes/pkg-descr ============================================================================== --- head/biology/mrbayes/pkg-descr Sat Feb 29 23:05:34 2020 (r527482) +++ head/biology/mrbayes/pkg-descr Sat Feb 29 23:24:39 2020 (r527483) @@ -8,4 +8,4 @@ impossible to calculate analytically; instead, MrBayes 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/ Added: head/biology/mrbayes/pkg-message ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/mrbayes/pkg-message Sat Feb 29 23:24:39 2020 (r527483) @@ -0,0 +1,8 @@ +[ +{ type: install + message: <<EOM +If MrBayes core dumps with "illegal hardware instruction (core dumped) mb", then +it should be built on the target system. +EOM +} +] Added: head/biology/mrbayes/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/mrbayes/pkg-plist Sat Feb 29 23:24:39 2020 (r527483) @@ -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
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