svn commit: r527483 - in head/biology/mrbayes: . files
Joseph Mingrone
jrm at FreeBSD.org
Sat Feb 29 23:24:42 UTC 2020
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 at 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 at m.u-tokyo.ac.jp
+MAINTAINER= mzaki at 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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