Update to 2.0.0-20100430

Rename port to mcmc-jags to avoid conflict with net/jags

PR:		ports/146180
Submitted by:	b.f. <bf1783 at gmail.com> (maintainer)

5 files changed, 113 insertions, 48 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index d2e78b868217..ebac02385887 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -6,22 +6,23 @@
 # $FreeBSD$
 #
 
-PORTNAME=	jags
-PORTVERSION=	1.0.4
-PORTREVISION=	1
+PORTNAME=	mcmc-jags
+DISTVERSION=	2.0.0-20100430
 CATEGORIES=	math
-MASTER_SITES=	http://www-fis.iarc.fr/~martyn/software/jags/
-DISTNAME=	${PORTNAME:U}-${PORTVERSION}
+MASTER_SITES=	SF:1,2,3
+MASTER_SITE_SUBDIR=	${PORTNAME}/JAGS/2.0/Source/:1 \
+		${PORTNAME}/Examples/2.0/:2 \
+		${PORTNAME}/Manuals/2.0/:3
+DISTFILES=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}:1
 .if !defined(NOPORTDOCS)
-DISTFILES=	${DISTNAME}${EXTRACT_SUFX} classic-bugs.tar.gz jags_user_manual.pdf
-EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
+DISTFILES+=	classic-bugs.tar.gz:2 jags_developer_manual.pdf:3 \
+		jags_installation_manual.pdf:3 jags_user_manual.pdf:3
+EXTRACT_ONLY=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}
 .endif
 
 MAINTAINER=	bf1783@gmail.com
 COMMENT=	Just Another Gibbs Sampler
 
-LIB_DEPENDS=	Rmath.0:${PORTSDIR}/math/libRmath
-
 .if defined(WITH_ATLAS)
 LIB_DEPENDS+=	atlas.2:${PORTSDIR}/math/atlas
 CONFIGURE_ARGS=	--with-lapack=-lalapack --with-blas=-lf77blas
@@ -32,27 +33,47 @@ CONFIGURE_ARGS=	--with-lapack=-llapack --with-blas=-lblas
 .endif
 
 DIST_SUBDIR=	${PORTNAME}
+WRKSRC=		${WRKDIR}/${PKGNAME:S/mcmc-//:U:R}
 
 GNU_CONFIGURE=	yes
-CONFIGURE_ENV=	LDFLAGS=-L${LOCALBASE}/lib
+CPPFLAGS+=	-I${LOCALBASE}/include
+LDFLAGS+=	-L${LOCALBASE}/lib
+CONFIGURE_ENV=	CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}"
 USE_FORTRAN=	yes
 USE_LDCONFIG=	yes
+USE_BISON=	build
 
 post-patch:
 	${REINPLACE_CMD} -e 's|[(]libdir[)]/pkgconfig|(prefix)/libdata/pkgconfig|g' \
 		${WRKSRC}/etc/Makefile.in
+	${REINPLACE_CMD} \
+		-e '/@WINDOWS_FALSE@bin_SCRIPTS =/s/jags/mcmc-&/' \
+		-e '/CLEANFILES =/s/jags/mcmc-&/' \
+		-e '/@WINDOWS_FALSE@jags:/s/jags/mcmc-&/' \
+		-e '/@WINDOWS_FALSE@.*rm -f jags/s/jags/mcmc-&/' \
+		-e '/@WINDOWS_FALSE@.*mv jags.tmp jags/s/jags/mcmc-&/2' \
+		${WRKSRC}/src/terminal/Makefile.in
 
 post-install:
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_user_manual.pdf \
+.for _M in developer installation user
+	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_${_M}_manual.pdf \
 		${DOCSDIR}
+.endfor
 .endif
 .if !defined(NOPORTEXAMPLES)
 	${MKDIR} ${EXAMPLESDIR}
 	( cd ${EXAMPLESDIR}; \
 	  ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/classic-bugs.tar.gz \
 	    -s ':^classic-bugs/*::' )
+	${SED} -i '' \
+		-e '\|JAGS ?=|{s|/usr/local|${PREFIX}|;s|jags|mcmc-&|;}' \
+		${EXAMPLESDIR}/vol[12]/Makefile
+	@${ECHO_MSG} ""
+	@${CAT} ${PKGMESSAGE}
+	@${ECHO_MSG} ""
+
 .endif
 
 .include <bsd.port.mk>
diff --git a/math/jags/distinfo b/math/jags/distinfo
index cf9925ae97de..ffe9c2ec8269 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,9 +1,15 @@
-MD5 (jags/JAGS-1.0.4.tar.gz) = a44dc20d548c5fd1a80504eb29f5397d
-SHA256 (jags/JAGS-1.0.4.tar.gz) = 14665d034a36120ad373bc85702cca443da8e540533509486bdef432db0b5cca
-SIZE (jags/JAGS-1.0.4.tar.gz) = 1074964
-MD5 (jags/classic-bugs.tar.gz) = 34291e2f6d3921b1b1eb0ac1db3fbf90
-SHA256 (jags/classic-bugs.tar.gz) = e3766060e0fcda709bf9326db79b14a6312f569417b7d59015bd37f0ebc1fe2f
-SIZE (jags/classic-bugs.tar.gz) = 81668
-MD5 (jags/jags_user_manual.pdf) = 018dbd12091a325bb3db92bf96b75283
-SHA256 (jags/jags_user_manual.pdf) = cc2ff991069258eae8c1f7c337b2f184678d923a508b040e3444104e87a0a72c
-SIZE (jags/jags_user_manual.pdf) = 247588
+MD5 (mcmc-jags/JAGS-2.0.0-20100430.tar.gz) = 0e027c98a7f3ade409a10b5b7ebd0e35
+SHA256 (mcmc-jags/JAGS-2.0.0-20100430.tar.gz) = 9bffe5ebee0896125bf497f22c88f1a751487ed9500f3ddf71bf63fd72d697fc
+SIZE (mcmc-jags/JAGS-2.0.0-20100430.tar.gz) = 1169874
+MD5 (mcmc-jags/classic-bugs.tar.gz) = 7df4366dfb5278cbd4ce43f21b4d9e6c
+SHA256 (mcmc-jags/classic-bugs.tar.gz) = 3814414bb5d23b1757f85cea549561389cf6d514cecad9a9ef945e21f806c3af
+SIZE (mcmc-jags/classic-bugs.tar.gz) = 81193
+MD5 (mcmc-jags/jags_developer_manual.pdf) = 850864bef54ff17858f8bf341b0c13c1
+SHA256 (mcmc-jags/jags_developer_manual.pdf) = 09d06b202adcbc9a52bd889c19c741ffb13f68b6657b9a0a999ad3f89259eb19
+SIZE (mcmc-jags/jags_developer_manual.pdf) = 71199
+MD5 (mcmc-jags/jags_installation_manual.pdf) = 42a78397a85100d2cfbde4c92aad3b9f
+SHA256 (mcmc-jags/jags_installation_manual.pdf) = d7147c7a57a1e55305c48bcbefbffd19090e958cc55339160c46401fa1d5955a
+SIZE (mcmc-jags/jags_installation_manual.pdf) = 119855
+MD5 (mcmc-jags/jags_user_manual.pdf) = efe47f0332544809627f57c209ca2068
+SHA256 (mcmc-jags/jags_user_manual.pdf) = 39f642e407a03c2e335adef5fca6af09ae5f9af312274dbb535b652c183b1aff
+SIZE (mcmc-jags/jags_user_manual.pdf) = 221001
diff --git a/math/jags/files/patch-src_terminal_parser.yy b/math/jags/files/patch-src_terminal_parser.yy
new file mode 100644
index 000000000000..9a9cbbedee53
--- /dev/null
+++ b/math/jags/files/patch-src_terminal_parser.yy
@@ -0,0 +1,10 @@
+--- src/terminal/parser.yy.orig	2010-04-30 03:22:53.000000000 -0400
++++ src/terminal/parser.yy	2010-04-30 03:23:09.000000000 -0400
+@@ -6,6 +6,7 @@
+ //#include <limits.h>
+ //#include <unistd.h>
+ 
++#include <climits>
+ #include <cstdlib>
+ #include <cstdio>
+ #include <iostream>
diff --git a/math/jags/pkg-message b/math/jags/pkg-message
new file mode 100644
index 000000000000..a7919a17c834
--- /dev/null
+++ b/math/jags/pkg-message
@@ -0,0 +1,3 @@
+Please note that the name of the jags script has been changed
+from "jags" to "mcmc-jags" on this platform, to avoid a conflict 
+with net/jags, and usage should be adjusted accordingly.
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index 332d4af3b458..37e3ecc2f464 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -1,4 +1,4 @@
-bin/jags
+bin/mcmc-jags
 include/JAGS/Console.h
 include/JAGS/JRmath.h
 include/JAGS/Module.h
@@ -9,44 +9,63 @@ include/JAGS/compiler/CounterTab.h
 include/JAGS/compiler/LogicalFactory.h
 include/JAGS/compiler/MixtureFactory.h
 include/JAGS/compiler/NodeFactory.h
+include/JAGS/compiler/ObsFuncTab.h
 include/JAGS/compiler/ParseTree.h
-include/JAGS/distribution/DistScalar.h
-include/JAGS/distribution/DistScalarRmath.h
+include/JAGS/distribution/ArrayDist.h
+include/JAGS/distribution/DistPtr.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/distribution/ScalarDist.h
+include/JAGS/distribution/TruncatedNormal.h
+include/JAGS/distribution/VectorDist.h
+include/JAGS/function/ArrayFunction.h
 include/JAGS/function/FuncTab.h
 include/JAGS/function/Function.h
-include/JAGS/function/InverseLinkFunc.h
-include/JAGS/function/ScalarFunc.h
+include/JAGS/function/FunctionPtr.h
+include/JAGS/function/LinkFunction.h
+include/JAGS/function/ScalarFunction.h
+include/JAGS/function/VectorFunction.h
 include/JAGS/graph/AggNode.h
+include/JAGS/graph/ArrayLogicalNode.h
+include/JAGS/graph/ArrayStochasticNode.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/LinkNode.h
 include/JAGS/graph/LogicalNode.h
 include/JAGS/graph/MixtureNode.h
 include/JAGS/graph/Node.h
 include/JAGS/graph/NodeError.h
+include/JAGS/graph/ScalarLogicalNode.h
+include/JAGS/graph/ScalarStochasticNode.h
 include/JAGS/graph/StochasticNode.h
+include/JAGS/graph/VSLogicalNode.h
+include/JAGS/graph/VectorLogicalNode.h
+include/JAGS/graph/VectorStochasticNode.h
 include/JAGS/model/BUGSModel.h
 include/JAGS/model/Model.h
 include/JAGS/model/Monitor.h
+include/JAGS/model/MonitorControl.h
 include/JAGS/model/MonitorFactory.h
+include/JAGS/model/MonitorInfo.h
 include/JAGS/model/NodeArray.h
 include/JAGS/model/SymTab.h
-include/JAGS/sampler/DensityMethod.h
-include/JAGS/sampler/DensitySampler.h
+include/JAGS/sampler/GraphView.h
 include/JAGS/sampler/Linear.h
 include/JAGS/sampler/Metropolis.h
+include/JAGS/sampler/ParallelSampler.h
 include/JAGS/sampler/RWMetropolis.h
+include/JAGS/sampler/SampleMethod.h
 include/JAGS/sampler/Sampler.h
 include/JAGS/sampler/SamplerFactory.h
 include/JAGS/sampler/SingletonFactory.h
 include/JAGS/sampler/Slicer.h
+include/JAGS/sampler/StepAdapter.h
+include/JAGS/sampler/TemperedMetropolis.h
 include/JAGS/sarray/Range.h
 include/JAGS/sarray/RangeIterator.h
 include/JAGS/sarray/SArray.h
@@ -54,24 +73,31 @@ 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
+include/JAGS/version.h
+lib/JAGS/modules-2.0.0/basemod.la
+lib/JAGS/modules-2.0.0/basemod.so
+lib/JAGS/modules-2.0.0/bugs.la
+lib/JAGS/modules-2.0.0/bugs.so
+lib/JAGS/modules-2.0.0/dic.la
+lib/JAGS/modules-2.0.0/dic.so
+lib/JAGS/modules-2.0.0/glm.la
+lib/JAGS/modules-2.0.0/glm.so
+lib/JAGS/modules-2.0.0/lecuyer.la
+lib/JAGS/modules-2.0.0/lecuyer.so
+lib/JAGS/modules-2.0.0/mix.la
+lib/JAGS/modules-2.0.0/mix.so
+lib/JAGS/modules-2.0.0/msm.la
+lib/JAGS/modules-2.0.0/msm.so
 lib/libjags.la
 lib/libjags.so
-lib/libjags.so.1
+lib/libjags.so.2
 lib/libjrmath.la
 lib/libjrmath.so
 lib/libjrmath.so.0
 libdata/pkgconfig/jags.pc
 libexec/jags-terminal
+%%PORTDOCS%%%%DOCSDIR%%/jags_developer_manual.pdf
+%%PORTDOCS%%%%DOCSDIR%%/jags_installation_manual.pdf
 %%PORTDOCS%%%%DOCSDIR%%/jags_user_manual.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/R/Rcheck.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/R/bench.R
@@ -105,18 +131,16 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/dyes.bug
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/test1.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/BT-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/ReadMe
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/bench-test1.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/bench.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/epil-data.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/epil-inits.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/epil2.bug
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/epil3.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/make-BT.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/notest1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/notest2.cmd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/test1.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/test1.cmd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/test2.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/test2.cmd
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/ReadMe
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/bench-test1.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/bench-test2.R
@@ -134,7 +158,6 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/test1.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/ReadMe
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/bench.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney-data.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney-init.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney.bug
@@ -216,11 +239,11 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/test1.cmd
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/test2.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/test2.cmd
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/bench-test1.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/bench-test2.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/bench-test3.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/bench-test4.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/bench-test5.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/notest1.cmd
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seeds-data.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seeds-init.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seeds.bug
@@ -228,6 +251,8 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seedssig.bug
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seedsuni.bug
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seedszro.bug
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test1.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test1.cmd
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test2.R
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test2.cmd
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test3.R
@@ -431,7 +456,7 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/R
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm lib/JAGS/modules
+@dirrm lib/JAGS/modules-2.0.0
 @dirrm lib/JAGS
 @dirrm include/JAGS/util
 @dirrm include/JAGS/sarray