6 files changed, 94 insertions, 91 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index 7d51506eae31..dfdc10179a79 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -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>
 #
 # $FreeBSD$
 #
 
 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 @@ DISTFILES=	${DISTNAME}${EXTRACT_SUFX} bugs-examples.tar.gz manual.pdf
 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:${PORTSDIR}/math/libRmath
@@ -28,21 +29,25 @@ LIB_DEPENDS+=	lapack.3:${PORTSDIR}/math/lapack
 CONFIGURE_ARGS=	--with-lapack=-llapack --with-blas=-lblas
 .endif
 
-USE_BISON=	yes
-
 DIST_SUBDIR=	${PORTNAME}
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	CPPFLAGS=-I${PREFIX}/include LDFLAGS=-L${PREFIX}/lib
 
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 500000
+BROKEN=		"Does not compile on 4.x"
+.endif
+
 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/*::' )
 .endif
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/math/jags/distinfo b/math/jags/distinfo
index 0c0bfa5d7136..587b2d4aa666 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -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
diff --git a/math/jags/files/patch-src-lib-model-Model.cc b/math/jags/files/patch-src-lib-model-Model.cc
deleted file mode 100644
index 357d1ece21b3..000000000000
--- a/math/jags/files/patch-src-lib-model-Model.cc
+++ /dev/null
@@ -1,19 +0,0 @@
---- src/lib/model/Model.cc.orig	Tue Aug 31 13:22:19 2004
-+++ src/lib/model/Model.cc	Tue Aug 31 13:22:28 2004
-@@ -12,14 +12,14 @@
- #include <sarray/RightRangeIterator.h>
- #include <sarray/LeftRangeIterator.h>
- 
--#include <Rmath.h>
--
- #include <iostream>
- #include <fstream>
- #include <sstream>
- #include <set>
- #include <stdexcept>
- #include <string>
-+
-+#include <Rmath.h>
- 
- using std::vector;
- using std::list;
diff --git a/math/jags/files/patch-src-terminal-parser.yy b/math/jags/files/patch-src-terminal-parser.yy
deleted file mode 100644
index f448825ef643..000000000000
--- a/math/jags/files/patch-src-terminal-parser.yy
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/terminal/parser.yy.orig	Tue Mar 30 09:43:35 2004
-+++ src/terminal/parser.yy	Thu May 27 16:59:09 2004
-@@ -3,6 +3,7 @@
- #include <iostream>
- #include <fstream>
- #include <map>
-+#include <time.h>
- #define MATHLIB_STANDALONE
- #include <Rmath.h>
- #include <JAGSVersion.h>
diff --git a/math/jags/pkg-descr b/math/jags/pkg-descr
index 0bb03bb175f5..e79a9f1dbb06 100644
--- a/math/jags/pkg-descr
+++ b/math/jags/pkg-descr
@@ -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
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index 437b72eb2965..590d9ceac3b3 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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 @@ lib/libjags.la
 %%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