Date: Fri, 14 May 2004 16:15:20 -0400 (EDT) From: Eric van Gyzen <vangyzen@stat.duke.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/66648: New Port: math/jags -- Just Another Gibbs Sampler Message-ID: <200405142015.i4EKFKWw008826@stat.duke.edu> Resent-Message-ID: <200405142020.i4EKK6lV043791@freefall.freebsd.org>
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>Number: 66648 >Category: ports >Synopsis: New Port: math/jags -- Just Another Gibbs Sampler >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri May 14 13:20:06 PDT 2004 >Closed-Date: >Last-Modified: >Originator: Eric van Gyzen >Release: FreeBSD 5.2-RELEASE i386 >Organization: Duke University Statistics >Environment: >Description: New Port: math/jags -- Just Another Gibbs Sampler Note that this port depends on the new math/libRmath port which I just submitted in PR ports/66644. >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # ports/math/jags # ports/math/jags/Makefile # ports/math/jags/pkg-descr # ports/math/jags/distinfo # ports/math/jags/pkg-plist # echo c - ports/math/jags mkdir -p ports/math/jags > /dev/null 2>&1 echo x - ports/math/jags/Makefile sed 's/^X//' >ports/math/jags/Makefile << 'END-of-ports/math/jags/Makefile' X# ex: ts=8 sts=0 noet X# Ports collection Makefile for: jags X# Date created: 21 April 2004 X# Whom: Eric van Gyzen <vangyzen@stat.duke.edu> X# X# $FreeBSD$ X# X XPORTNAME= jags XPORTVERSION= 0.50 XCATEGORIES= math XMASTER_SITES= http://www-fis.iarc.fr/~martyn/software/jags/ XDISTNAME= ${PORTNAME:U}-${PORTVERSION} X.if !defined(NOPORTDOCS) XDISTFILES= ${DISTNAME}${EXTRACT_SUFX} bugs-examples.tar.gz manual.pdf XEXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} X.endif X XMAINTAINER= vangyzen@stat.duke.edu XCOMMENT= Just Another Gibbs Sampler X XLIB_DEPENDS= Rmath.0:${PORTSDIR}/math/libRmath X X.if defined(WITH_ATLAS) XLIB_DEPENDS+= f77blas.1:${PORTSDIR}/math/atlas XCONFIGURE_ARGS= --with-lapack=-lalapack --with-blas=-lf77blas X.else XLIB_DEPENDS+= lapack.3:${PORTSDIR}/math/lapack XCONFIGURE_ARGS= --with-lapack=-llapack --with-blas=-lblas X.endif X XDIST_SUBDIR= ${PORTNAME} X XGNU_CONFIGURE= yes XCONFIGURE_ENV= CPPFLAGS=-I${PREFIX}/include LDFLAGS=-L${PREFIX}/lib X Xpost-install: X.if !defined(NOPORTDOCS) X ${MKDIR} ${DOCSDIR} X ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/manual.pdf ${DOCSDIR} X ${MKDIR} ${EXAMPLESDIR} X ( cd ${EXAMPLESDIR}; \ X ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/bugs-examples.tar.gz \ X -s ':^bugs-examples/*::' ) X.endif X X.include <bsd.port.mk> END-of-ports/math/jags/Makefile echo x - ports/math/jags/pkg-descr sed 's/^X//' >ports/math/jags/pkg-descr << 'END-of-ports/math/jags/pkg-descr' XJAGS is Just Another Gibbs Sampler -- a program for Bayesian analysis of Xgraphical models via Gibbs Sampling, not wholly unlike classic BUGS. X XThe functionality of JAGS is based on the BUGS program created by the XMRC Biostatistics Unit (http://www.mrc-bsu.cam.ac.uk/). There is a short Xmanual that describes the differences between JAGS and BUGS. X XThe manual is installed as /usr/local/share/doc/jags/manual.pdf. X XSome of the BUGS examples have been modified to run with JAGS, and have Xbeen turned into a test suite. They are installed under X/usr/local/share/examples/jags/. X XWWW: http://www-fis.iarc.fr/~martyn/software/jags/ END-of-ports/math/jags/pkg-descr echo x - ports/math/jags/distinfo sed 's/^X//' >ports/math/jags/distinfo << 'END-of-ports/math/jags/distinfo' XMD5 (jags/JAGS-0.50.tar.gz) = 13a068aa43b84f812e476129fbdb03db XMD5 (jags/bugs-examples.tar.gz) = c5baddf2f29bab79f8a6c7d0b3873727 XMD5 (jags/manual.pdf) = 8cc1b0371872472ea9bd496bfdbd49f4 XSIZE (jags/JAGS-0.50.tar.gz) = 481609 XSIZE (jags/bugs-examples.tar.gz) = 72373 XSIZE (jags/manual.pdf) = 130157 END-of-ports/math/jags/distinfo echo x - ports/math/jags/pkg-plist sed 's/^X//' >ports/math/jags/pkg-plist << 'END-of-ports/math/jags/pkg-plist' Xbin/jags Xinclude/JAGS/Console.h Xinclude/JAGS/JAGSVersion.h Xinclude/JAGS/distributions/DistDiscrete.h Xinclude/JAGS/distributions/DistFinite.h Xinclude/JAGS/distributions/DistReal.h Xinclude/JAGS/distributions/DistTab.h Xinclude/JAGS/distributions/Distribution.h Xinclude/JAGS/functions/FuncTab.h Xinclude/JAGS/functions/Function.h Xinclude/JAGS/functions/InverseLinkFunc.h Xinclude/JAGS/functions/ScalarArgScalarFunc.h Xinclude/JAGS/functions/ScalarFunc.h Xinclude/JAGS/graph/AggNode.h Xinclude/JAGS/graph/ConstantNode.h Xinclude/JAGS/graph/DeterministicNode.h Xinclude/JAGS/graph/Graph.h Xinclude/JAGS/graph/GraphMarks.h Xinclude/JAGS/graph/LogicalNode.h Xinclude/JAGS/graph/MixtureNode.h Xinclude/JAGS/graph/Node.h Xinclude/JAGS/graph/NodeError.h Xinclude/JAGS/graph/OffsetNode.h Xinclude/JAGS/graph/StochasticNode.h Xinclude/JAGS/graph/SubSetIndex.h Xinclude/JAGS/graph/SubSetNode.h Xinclude/JAGS/matrix/lapack.h Xinclude/JAGS/matrix/matexp.h Xinclude/JAGS/matrix/matrix.h Xinclude/JAGS/model/Compiler.h Xinclude/JAGS/model/Counter.h Xinclude/JAGS/model/CounterTab.h Xinclude/JAGS/model/LogicalFactory.h Xinclude/JAGS/model/Model.h Xinclude/JAGS/model/NodeArray.h Xinclude/JAGS/model/ParseTree.h Xinclude/JAGS/model/SymTab.h Xinclude/JAGS/model/TraceMonitor.h Xinclude/JAGS/model/parser.h Xinclude/JAGS/model/parser_extra.h Xinclude/JAGS/sampler/ConjugateBeta.h Xinclude/JAGS/sampler/ConjugateDirichlet.h Xinclude/JAGS/sampler/ConjugateFactory.h Xinclude/JAGS/sampler/ConjugateGamma.h Xinclude/JAGS/sampler/ConjugateMNormal.h Xinclude/JAGS/sampler/ConjugateNormal.h Xinclude/JAGS/sampler/ConjugateSampler.h Xinclude/JAGS/sampler/ConjugateWishart.h Xinclude/JAGS/sampler/FiniteFactory.h Xinclude/JAGS/sampler/FiniteSampler.h Xinclude/JAGS/sampler/GibbsFactory.h Xinclude/JAGS/sampler/GibbsSampler.h Xinclude/JAGS/sampler/Sampler.h Xinclude/JAGS/sampler/SamplerFactory.h Xinclude/JAGS/sampler/SliceFactory.h Xinclude/JAGS/sampler/SliceSampler.h Xinclude/JAGS/sarray/Index.h Xinclude/JAGS/sarray/LeftRangeIterator.h Xinclude/JAGS/sarray/Range.h Xinclude/JAGS/sarray/RightRangeIterator.h Xinclude/JAGS/sarray/SArray.h Xlib/libjags.a Xlib/libjags.la X%%PORTDOCS%%%%DOCSDIR%%/manual.pdf X%%PORTDOCS%%%%EXAMPLESDIR%%/R/bench.R X%%PORTDOCS%%%%EXAMPLESDIR%%/R/check.R X%%PORTDOCS%%%%EXAMPLESDIR%%/ReadMe 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X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/test1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/ReadMe X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-constant.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-inits.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-linear.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-quadratic.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test2.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test3.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/ReadMe X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-inits.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-inits.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.dat X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.in X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/test1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-inits.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/test1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-inits.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools.dat X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/ReadMe X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest1.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest2.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-data.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits1.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits2.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits3.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits4.R X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant2.bug X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test3.cmd X%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test4.cmd X@dirrm include/JAGS/sarray X@dirrm include/JAGS/sampler X@dirrm include/JAGS/model X@dirrm include/JAGS/matrix X@dirrm include/JAGS/graph X@dirrm include/JAGS/functions X@dirrm include/JAGS/distributions X@dirrm include/JAGS X%%PORTDOCS%%@dirrm %%DOCSDIR%% X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/stagnant X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/schools X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/pigs X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/orange X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/jaw X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/ice X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/hearts X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/eyes X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/dugongs X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/cervix X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/birats X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/biops X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/beetles X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/asia X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/alli X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/air X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2 X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/seeds X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/salm X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/rats X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/pump X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford/old X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/mice X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/lsat X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/litters X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/line X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/leuk X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/kidney X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/equiv X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/epil X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/dyes X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/bones X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/blocker X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1 X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/R X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% END-of-ports/math/jags/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted:
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