Attachment 57864 Details for Bug 87275 – file.diff

[patch] file.diff

file.diff (text/plain), 17.09 KB, created by eric on 2005-10-11 20:40:15 UTC

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Creator: eric

Created: 2005-10-11 20:40:15 UTC

Size: 17.09 KB

patch

obsolete

>Index: jags/Makefile
>===================================================================
>RCS file: /freebsd/cvsroot/ports/math/jags/Makefile,v
>retrieving revision 1.1
>diff -u -u -r1.1 Makefile
>--- jags/Makefile	27 May 2004 15:18:45 -0000	1.1
>+++ jags/Makefile	11 Oct 2005 01:55:50 -0000
>@@ -1,12 +1,13 @@
>-# Ports collection Makefile for:	jags
>-# Date created:				21 April 2004
>-# Whom:					Eric van Gyzen <vangyzen@stat.duke.edu>
>+# vim: tabstop=8 softtabstop=0 noexpandtab
>+# Ports Makefile for:	jags
>+# Date created:		21 April 2004
>+# Whom:			Eric van Gyzen <vangyzen@stat.duke.edu>
> #
> # $FreeBSD: ports/math/jags/Makefile,v 1.1 2004/05/27 15:18:45 pav Exp $
> #
> 
> PORTNAME=	jags
>-PORTVERSION=	0.50
>+PORTVERSION=	0.90
> CATEGORIES=	math
> MASTER_SITES=	http://www-fis.iarc.fr/~martyn/software/jags/
> DISTNAME=	${PORTNAME:U}-${PORTVERSION}
>@@ -15,7 +16,7 @@
> EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
> .endif
> 
>-MAINTAINER=	vangyzen@stat.duke.edu
>+MAINTAINER=	eric+fbports@vangyzen.net
> COMMENT=	Just Another Gibbs Sampler
> 
> LIB_DEPENDS=	Rmath.0:${PORTSDIR}/math/libRmath
>@@ -28,8 +29,6 @@
> CONFIGURE_ARGS=	--with-lapack=-llapack --with-blas=-lblas
> .endif
> 
>-USE_BISON=	yes
>-
> DIST_SUBDIR=	${PORTNAME}
> 
> GNU_CONFIGURE=	yes
>@@ -37,9 +36,9 @@
> 
> post-install:
> .if !defined(NOPORTDOCS)
>-	${MKDIR} ${DOCSDIR}
>+	${MKDIR} -p ${DOCSDIR}
> 	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/manual.pdf ${DOCSDIR}
>-	${MKDIR} ${EXAMPLESDIR}
>+	${MKDIR} -p ${EXAMPLESDIR}
> 	( cd ${EXAMPLESDIR}; \
> 	  ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/bugs-examples.tar.gz \
> 	    -s ':^bugs-examples/*::' )
>Index: jags/distinfo
>===================================================================
>RCS file: /freebsd/cvsroot/ports/math/jags/distinfo,v
>retrieving revision 1.1
>diff -u -u -r1.1 distinfo
>--- jags/distinfo	27 May 2004 15:18:45 -0000	1.1
>+++ jags/distinfo	8 Oct 2005 01:27:43 -0000
>@@ -1,6 +1,6 @@
>-MD5 (jags/JAGS-0.50.tar.gz) = 13a068aa43b84f812e476129fbdb03db
>-MD5 (jags/bugs-examples.tar.gz) = c5baddf2f29bab79f8a6c7d0b3873727
>-MD5 (jags/manual.pdf) = 8cc1b0371872472ea9bd496bfdbd49f4
>-SIZE (jags/JAGS-0.50.tar.gz) = 481609
>-SIZE (jags/bugs-examples.tar.gz) = 72373
>-SIZE (jags/manual.pdf) = 130157
>+MD5 (jags/JAGS-0.90.tar.gz) = 6e33e64de3073617867a2c27b7dbfb31
>+MD5 (jags/bugs-examples.tar.gz) = e7abd4d3234b2aec868720f6040804f0
>+MD5 (jags/manual.pdf) = cbd1068323afc07fd3d76529b4297bac
>+SIZE (jags/JAGS-0.90.tar.gz) = 522489
>+SIZE (jags/bugs-examples.tar.gz) = 277569 
>+SIZE (jags/manual.pdf) = 142220
>Index: jags/pkg-descr
>===================================================================
>RCS file: /freebsd/cvsroot/ports/math/jags/pkg-descr,v
>retrieving revision 1.1
>diff -u -u -r1.1 pkg-descr
>--- jags/pkg-descr	27 May 2004 15:18:45 -0000	1.1
>+++ jags/pkg-descr	8 Oct 2005 01:30:05 -0000
>@@ -1,5 +1,5 @@
>-JAGS is Just Another Gibbs Sampler -- a program for Bayesian analysis of
>-graphical models via Gibbs Sampling, not wholly unlike classic BUGS.
>+JAGS is Just Another Gibbs Sampler -- a program for analysis of
>+Bayesian hierarchical models using Gibbs sampling not wholly unlike BUGS.
> 
> The functionality of JAGS is based on the BUGS program created by the
> MRC Biostatistics Unit (http://www.mrc-bsu.cam.ac.uk/). There is a short
>Index: jags/pkg-plist
>===================================================================
>RCS file: /freebsd/cvsroot/ports/math/jags/pkg-plist,v
>retrieving revision 1.1
>diff -u -u -r1.1 pkg-plist
>--- jags/pkg-plist	27 May 2004 15:18:45 -0000	1.1
>+++ jags/pkg-plist	11 Oct 2005 01:57:19 -0000
>@@ -1,63 +1,56 @@
> bin/jags
> include/JAGS/Console.h
> include/JAGS/JAGSVersion.h
>+include/JAGS/compiler/Compiler.h
>+include/JAGS/compiler/ConstantFactory.h
>+include/JAGS/compiler/Counter.h
>+include/JAGS/compiler/CounterTab.h
>+include/JAGS/compiler/LogicalFactory.h
>+include/JAGS/compiler/MixtureFactory.h
>+include/JAGS/compiler/NodeFactory.h
>+include/JAGS/compiler/ParseTree.h
>+include/JAGS/compiler/parser.h
>+include/JAGS/compiler/parser_extra.h
> include/JAGS/distributions/DistDiscrete.h
>-include/JAGS/distributions/DistFinite.h
> include/JAGS/distributions/DistReal.h
> include/JAGS/distributions/DistTab.h
> include/JAGS/distributions/Distribution.h
> include/JAGS/functions/FuncTab.h
> include/JAGS/functions/Function.h
> include/JAGS/functions/InverseLinkFunc.h
>-include/JAGS/functions/ScalarArgScalarFunc.h
> include/JAGS/functions/ScalarFunc.h
> include/JAGS/graph/AggNode.h
> include/JAGS/graph/ConstantNode.h
> include/JAGS/graph/DeterministicNode.h
>+include/JAGS/graph/DevianceNode.h
> include/JAGS/graph/Graph.h
> include/JAGS/graph/GraphMarks.h
> include/JAGS/graph/LogicalNode.h
> include/JAGS/graph/MixtureNode.h
> include/JAGS/graph/Node.h
> include/JAGS/graph/NodeError.h
>-include/JAGS/graph/OffsetNode.h
>+include/JAGS/graph/NodeNameTab.h
> include/JAGS/graph/StochasticNode.h
>-include/JAGS/graph/SubSetIndex.h
>-include/JAGS/graph/SubSetNode.h
> include/JAGS/matrix/lapack.h
> include/JAGS/matrix/matexp.h
> include/JAGS/matrix/matrix.h
>-include/JAGS/model/Compiler.h
>-include/JAGS/model/Counter.h
>-include/JAGS/model/CounterTab.h
>-include/JAGS/model/LogicalFactory.h
>+include/JAGS/model/BUGSModel.h
> include/JAGS/model/Model.h
> include/JAGS/model/NodeArray.h
>-include/JAGS/model/ParseTree.h
> include/JAGS/model/SymTab.h
> include/JAGS/model/TraceMonitor.h
>-include/JAGS/model/parser.h
>-include/JAGS/model/parser_extra.h
>-include/JAGS/sampler/ConjugateBeta.h
>-include/JAGS/sampler/ConjugateDirichlet.h
> include/JAGS/sampler/ConjugateFactory.h
>-include/JAGS/sampler/ConjugateGamma.h
>-include/JAGS/sampler/ConjugateMNormal.h
>-include/JAGS/sampler/ConjugateNormal.h
>-include/JAGS/sampler/ConjugateSampler.h
>-include/JAGS/sampler/ConjugateWishart.h
>+include/JAGS/sampler/DSumFactory.h
> include/JAGS/sampler/FiniteFactory.h
>-include/JAGS/sampler/FiniteSampler.h
> include/JAGS/sampler/GibbsFactory.h
> include/JAGS/sampler/GibbsSampler.h
> include/JAGS/sampler/Sampler.h
> include/JAGS/sampler/SamplerFactory.h
> include/JAGS/sampler/SliceFactory.h
>-include/JAGS/sampler/SliceSampler.h
>+include/JAGS/sampler/Slicer.h
> include/JAGS/sarray/Index.h
>-include/JAGS/sarray/LeftRangeIterator.h
> include/JAGS/sarray/Range.h
>-include/JAGS/sarray/RightRangeIterator.h
>+include/JAGS/sarray/RangeIterator.h
> include/JAGS/sarray/SArray.h
> lib/libjags.a
> lib/libjags.la
>@@ -90,6 +83,7 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/dyes-init.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/dyes.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/epil/.Rhistory
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/epil/BT-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/epil/ReadMe
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/epil/bench-test1.R
>@@ -111,16 +105,19 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/equivmiss-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/test2.cmd
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/bench-test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler-data.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler-inits.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler.bug
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/bench.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/kidney-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/kidney-init.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/kidney.bug
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/kidney.bug.new
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/bench-test1.R
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/data-transform.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leuk-data.R
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leuk-data2.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leuk-init.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leuk-poisson.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leuk-s.dat
>@@ -144,8 +141,6 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/ReadMe
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/bench-test1.R
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/bench-test2.R
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat-data-transformed.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat-init.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat.bug
>@@ -154,7 +149,6 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat2.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/notest2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/test1.cmd
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/transform-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/mice-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/mice-init.R
>@@ -190,11 +184,13 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/salm.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test2.cmd
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/bench-test2.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/bench-test3.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/bench-test4.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/bench-test5.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/jags2.ind
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/jags2.out
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seeds-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seeds-init.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seeds.bug
>@@ -202,7 +198,6 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seedssig.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seedsuni.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/seedszro.bug
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test3.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test4.cmd
>@@ -212,15 +207,20 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/air-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/air-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/air.bug
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/bench.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/alli-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/alli-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/alli.bug
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia2-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia2.bug
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/bench-test2.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/test2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/beetles-cloglog.bug
>@@ -228,14 +228,23 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/beetles-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/beetles-logit.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/beetles-probit.bug
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/bench-test2.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/bench-test3.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/test2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/beetles/test3.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/biops-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/biops-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/biops.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/biops/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/bar.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/bench-test2.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/bench-test3.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/bench-test4.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/birats-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/birats-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/birats1.bug
>@@ -247,15 +256,19 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/test3.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/birats/test4.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/bar
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/baz
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/cervix-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/cervix-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/cervix.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/cervix/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/dugongs/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/dugongs/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/bench-test2.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/eyes-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/eyes-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/eyes.bug
>@@ -263,17 +276,23 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/eyes2.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/eyes/test2.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/hearts-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/hearts-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/hearts.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/hearts.dat
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/hearts/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/bench.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/ice-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/ice-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/icear.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/ice/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/bench-test2.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/bench-test3.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-constant.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/jaw-inits.R
>@@ -283,19 +302,23 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test3.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/bench-test1.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/bench.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/mvotree.bug
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/orange-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.dat
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/otree.in
>-%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/orange/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/test1.cmd
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/bench-test1.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-data.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools-inits.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/schools.bug
>@@ -303,6 +326,8 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/schools/test1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/ReadMe
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/bench-test3.R
>+%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/bench-test4.R
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest1.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/notest2.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-data.R
>@@ -314,15 +339,6 @@
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant2.bug
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test3.cmd
> %%PORTDOCS%%%%EXAMPLESDIR%%/vol2/stagnant/test4.cmd
>-@dirrm include/JAGS/sarray
>-@dirrm include/JAGS/sampler
>-@dirrm include/JAGS/model
>-@dirrm include/JAGS/matrix
>-@dirrm include/JAGS/graph
>-@dirrm include/JAGS/functions
>-@dirrm include/JAGS/distributions
>-@dirrm include/JAGS
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/stagnant
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/schools
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol2/pigs
>@@ -352,6 +368,7 @@
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/line
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/leuk
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/kidney
>+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/inhaler
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/equiv
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/epil
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/dyes
>@@ -360,3 +377,13 @@
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/R
> %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%
>+@dirrm include/JAGS/sarray
>+@dirrm include/JAGS/sampler
>+@dirrm include/JAGS/model
>+@dirrm include/JAGS/matrix
>+@dirrm include/JAGS/graph
>+@dirrm include/JAGS/functions
>+@dirrm include/JAGS/distributions
>+@dirrm include/JAGS/compiler
>+@dirrm include/JAGS

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Attachments on bug 87275: 57864