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Update from version 0.90 to 1.0.3, which appears to fix a compilation

Browse source 
problem.  Also removed F77 from CONFIGURE_ENV.  Resign maintainership,
moving to ports@FreeBSD.org.

Submitted by:	Eric van Gyzen <eric+fbports@vangyzen.net> (maintainer)
This commit is contained in:
Gerald Pfeifer 2009-01-19 01:19:07 +00:00
parent 1ef00cf0dd
commit b7a6bfafd9
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=226409
4 changed files with 94 additions and 61 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

18
math/jags/Makefile
View file

@ -1,5 +1,5 @@
# vim: tabstop=8 softtabstop=0 noexpandtab
# Ports Makefile for: jags
# Ports collection Makefile for: jags
# Date created: 21 April 2004
# Whom: Eric van Gyzen <vangyzen@stat.duke.edu>
#
@ -7,17 +7,16 @@
#
PORTNAME= jags
PORTVERSION= 0.90
PORTREVISION= 3
PORTVERSION= 1.0.3
CATEGORIES= math
MASTER_SITES= http://www-fis.iarc.fr/~martyn/software/jags/
DISTNAME= ${PORTNAME:U}-${PORTVERSION}
.if !defined(NOPORTDOCS)
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} bugs-examples.tar.gz manual.pdf
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} classic-bugs.tar.gz jags_user_manual.pdf
EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX}
.endif
MAINTAINER= eric+fbports@vangyzen.net
MAINTAINER= ports@FreeBSD.org
COMMENT= Just Another Gibbs Sampler
LIB_DEPENDS= Rmath.0:${PORTSDIR}/math/libRmath
@ -34,17 +33,18 @@ CONFIGURE_ARGS= --with-lapack=-llapack --with-blas=-lblas
DIST_SUBDIR= ${PORTNAME}
GNU_CONFIGURE= yes
CONFIGURE_ENV= CPPFLAGS=-I${PREFIX}/include LDFLAGS=-L${PREFIX}/lib F77="${F77}"
CONFIGURE_ENV= LDFLAGS=-L${PREFIX}/lib
USE_FORTRAN= yes
post-install:
.if !defined(NOPORTDOCS)
${MKDIR} ${DOCSDIR}
${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/manual.pdf ${DOCSDIR}
${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_user_manual.pdf \
${DOCSDIR}
${MKDIR} ${EXAMPLESDIR}
( cd ${EXAMPLESDIR}; \
${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/bugs-examples.tar.gz \
-s ':^bugs-examples/*::' )
${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/classic-bugs.tar.gz \
-s ':^classic-bugs/*::' )
.endif
.include <bsd.port.mk>

18
math/jags/distinfo
View file

@ -1,9 +1,9 @@
MD5 (jags/JAGS-0.90.tar.gz) = 6e33e64de3073617867a2c27b7dbfb31
SHA256 (jags/JAGS-0.90.tar.gz) = 19990790f6c19262c7d6f32fd414588dbd3e9cece21fea8f0c34eb39a2ddcbd1
SIZE (jags/JAGS-0.90.tar.gz) = 522489
MD5 (jags/bugs-examples.tar.gz) = e7abd4d3234b2aec868720f6040804f0
SHA256 (jags/bugs-examples.tar.gz) = eff04a699dce84e49638bd826238cfbff1beeb6c0b59803bb7404aab4d8be5ab
SIZE (jags/bugs-examples.tar.gz) = 277569
MD5 (jags/manual.pdf) = cbd1068323afc07fd3d76529b4297bac
SHA256 (jags/manual.pdf) = 2f4941639b5aa8e6e5a7735f562216e30f6f9dc0cfeba16408a480354b68c030
SIZE (jags/manual.pdf) = 142220
MD5 (jags/JAGS-1.0.3.tar.gz) = fa94031290e23d47e26affc571f76e38
SHA256 (jags/JAGS-1.0.3.tar.gz) = 066e01617adb483d71d4bdefedba432babb7430379952910260f4f264fb0ef2e
SIZE (jags/JAGS-1.0.3.tar.gz) = 1204624
MD5 (jags/classic-bugs.tar.gz) = a9079cc43b8d694d8f53640816a86ab2
SHA256 (jags/classic-bugs.tar.gz) = c951b2d2f9631b71bfed1877368b0010f30130c6089f14724005463b4f605223
SIZE (jags/classic-bugs.tar.gz) = 80405
MD5 (jags/jags_user_manual.pdf) = ad968d6ba080c63447fe5e55a210ed86
SHA256 (jags/jags_user_manual.pdf) = 286066261d234e5d68233b92e0c29e0396d6f5f3d43392aeeb1725084ae9985b
SIZE (jags/jags_user_manual.pdf) = 247342

2
math/jags/pkg-descr
View file

@ -5,7 +5,7 @@ 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
manual that describes the differences between JAGS and BUGS.
The manual is installed as /usr/local/share/doc/jags/manual.pdf.
The manual is installed as /usr/local/share/doc/jags/jags_user_manual.pdf.
Some of the BUGS examples have been modified to run with JAGS, and have
been turned into a test suite. They are installed under

117
math/jags/pkg-plist
View file

@ -1,6 +1,7 @@
bin/jags
include/JAGS/Console.h
include/JAGS/JAGSVersion.h
include/JAGS/JRmath.h
include/JAGS/Module.h
include/JAGS/compiler/Compiler.h
include/JAGS/compiler/ConstantFactory.h
include/JAGS/compiler/Counter.h
@ -9,16 +10,17 @@ 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/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/ScalarFunc.h
include/JAGS/distribution/DistScalar.h
include/JAGS/distribution/DistScalarRmath.h
include/JAGS/distribution/DistTab.h
include/JAGS/distribution/Distribution.h
include/JAGS/distribution/RNG.h
include/JAGS/distribution/RNGFactory.h
include/JAGS/distribution/RmathRNG.h
include/JAGS/function/FuncTab.h
include/JAGS/function/Function.h
include/JAGS/function/InverseLinkFunc.h
include/JAGS/function/ScalarFunc.h
include/JAGS/graph/AggNode.h
include/JAGS/graph/ConstantNode.h
include/JAGS/graph/DeterministicNode.h
@ -29,32 +31,49 @@ include/JAGS/graph/LogicalNode.h
include/JAGS/graph/MixtureNode.h
include/JAGS/graph/Node.h
include/JAGS/graph/NodeError.h
include/JAGS/graph/NodeNameTab.h
include/JAGS/graph/StochasticNode.h
include/JAGS/matrix/lapack.h
include/JAGS/matrix/matexp.h
include/JAGS/matrix/matrix.h
include/JAGS/model/BUGSModel.h
include/JAGS/model/Model.h
include/JAGS/model/Monitor.h
include/JAGS/model/MonitorFactory.h
include/JAGS/model/NodeArray.h
include/JAGS/model/SymTab.h
include/JAGS/model/TraceMonitor.h
include/JAGS/sampler/ConjugateFactory.h
include/JAGS/sampler/DSumFactory.h
include/JAGS/sampler/FiniteFactory.h
include/JAGS/sampler/GibbsFactory.h
include/JAGS/sampler/GibbsSampler.h
include/JAGS/sampler/DensityMethod.h
include/JAGS/sampler/DensitySampler.h
include/JAGS/sampler/Linear.h
include/JAGS/sampler/Metropolis.h
include/JAGS/sampler/RWMetropolis.h
include/JAGS/sampler/Sampler.h
include/JAGS/sampler/SamplerFactory.h
include/JAGS/sampler/SliceFactory.h
include/JAGS/sampler/SingletonFactory.h
include/JAGS/sampler/Slicer.h
include/JAGS/sarray/Index.h
include/JAGS/sarray/Range.h
include/JAGS/sarray/RangeIterator.h
include/JAGS/sarray/SArray.h
lib/libjags.a
include/JAGS/util/dim.h
include/JAGS/util/integer.h
include/JAGS/util/logical.h
include/JAGS/util/nainf.h
lib/JAGS/modules/basemod.la
lib/JAGS/modules/basemod.so
lib/JAGS/modules/bugs.la
lib/JAGS/modules/bugs.so
lib/JAGS/modules/dic.la
lib/JAGS/modules/dic.so
lib/JAGS/modules/mix.la
lib/JAGS/modules/mix.so
lib/JAGS/modules/msm.la
lib/JAGS/modules/msm.so
lib/libjags.la
%%PORTDOCS%%%%DOCSDIR%%/manual.pdf
lib/libjags.so
lib/libjags.so.1
lib/libjrmath.la
lib/libjrmath.so
lib/libjrmath.so.0
lib/pkgconfig/jags.pc
libexec/jags-terminal
%%PORTDOCS%%%%DOCSDIR%%/jags_user_manual.pdf
%%PORTDOCS%%%%EXAMPLESDIR%%/R/Rcheck.R
%%PORTDOCS%%%%EXAMPLESDIR%%/R/bench.R
%%PORTDOCS%%%%EXAMPLESDIR%%/R/check.R
%%PORTDOCS%%%%EXAMPLESDIR%%/ReadMe
@ -72,18 +91,20 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/blockht.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/notest2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/notest3.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/blocker/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bones-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bones-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/bones.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/bones/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/dyes-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/dyes-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/dyes.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/dyes/test1.R
%%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
@ -103,12 +124,14 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/equiv-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/equiv.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/equivmiss-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/equiv/test2.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/inhaler/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/ReadMe
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/kidney/bench.R
@ -127,46 +150,52 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.dat
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.in
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/leuk/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/line-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/line-inits.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/line.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/line/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/ReadMe
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/litters-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/litters-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/litters.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/litters/test1.R
%%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.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat.dat
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat2-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/lsat2.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/notest2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/test2.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/lsat/test2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/mice-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/mice-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/mice.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/mice/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/ReadMe
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/old/oxford.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/old/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/oxford-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/oxford-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/oxford.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/oxford.dat
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/oxford/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/pump-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/pump-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/pump.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/pump/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/bench-test2.R
@ -174,6 +203,7 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/rats-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/rats.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/ratsmiss-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/rats/test2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/bench-test1.R
@ -182,14 +212,14 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/salm-init.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/salm-pareto.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/salm.bug
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test2.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/salm/test2.cmd
%%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
@ -198,9 +228,13 @@ 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/test2.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test3.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test3.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test4.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test4.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test5.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol1/seeds/test5.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/Makefile
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/air/ReadMe
@ -214,6 +248,7 @@ lib/libjags.la
%%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.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/alli/test1.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/asia/asia.bug
@ -240,7 +275,6 @@ lib/libjags.la
%%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
@ -256,8 +290,6 @@ 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
@ -301,18 +333,18 @@ lib/libjags.la
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/jaw/test1.cmd
%%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/bench-test2.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/orange/test2.cmd
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/bench-test1.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-data.R
%%PORTDOCS%%%%EXAMPLESDIR%%/vol2/pigs/pigs-inits.R
@ -360,7 +392,6 @@ lib/libjags.la
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/salm
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/rats
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/pump
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford/old
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/oxford
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/mice
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/vol1/lsat
@ -378,12 +409,14 @@ lib/libjags.la
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/R
%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm lib/JAGS/modules
@dirrm lib/JAGS
@dirrm include/JAGS/util
@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/function
@dirrm include/JAGS/distribution
@dirrm include/JAGS/compiler
@dirrm include/JAGS