math/jags: 3.4.0 -> 4.0.0

- New WWW
- Changes:
  https://martynplummer.wordpress.com/2015/08/02/whats-new-in-jags-4-0-0-part-14-reproducibility-and-testing/
  https://martynplummer.wordpress.com/2015/08/09/whats-new-in-jags-4-0-0-part-24-dealing-with-undefined-nodes/
  https://martynplummer.wordpress.com/2015/08/16/whats-new-in-jags-4-0-0-part-34-r-style-features/#more-353

PR:		204525
Submitted by:	Rainer Hurling <rhurlin@gwdg.de>
Approved by:	bf

3 files changed, 36 insertions, 22 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index 1b9d8e51cb8e..e7d74de448b4 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -2,14 +2,14 @@
 # $FreeBSD$
 
 PORTNAME=	mcmc-jags
-PORTVERSION=	3.4.0
-PORTREVISION=	4
+PORTVERSION=	4.0.0
 CATEGORIES=	math
 MASTER_SITES=	SF/mcmc-jags/JAGS/${S}.x/Source/:1 \
 		SF/mcmc-jags/Examples/${S}.x/:2 \
 		SF/mcmc-jags/Manuals/2.x/:3 \
 		SF/mcmc-jags/Manuals/${S}.x/:4
 DISTFILES=	JAGS-${PORTVERSION}${EXTRACT_SUFX}:1
+DIST_SUBDIR=	${PORTNAME}
 EXTRACT_ONLY=	${DISTFILES:M*[12]:C|:.*||}
 
 MAINTAINER=	bf@FreeBSD.org
@@ -18,14 +18,12 @@ COMMENT=	Just Another Gibbs Sampler
 LICENSE=	GPLv2
 
 GNU_CONFIGURE=	yes
-USES=		bison fortran gmake libtool
+USES=		bison compiler:features fortran gmake libtool localbase
+USE_GCC=	yes
 USE_LDCONFIG=	yes
 
-DIST_SUBDIR=	${PORTNAME}
 WRKSRC=		${WRKDIR}/JAGS-${PORTVERSION}
 
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
 PLIST_SUB=	MODULEVERSION=${S}
 S=		${PORTVERSION:C|\..*||}
 
@@ -57,7 +55,7 @@ LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
 LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
 CONFIGURE_ARGS=	--with-lapack="-llapack" --with-blas="-lblas"
 .else
-IGNORE=		: invalid value for WITH_BLAS: ${WITH_BLAS}
+IGNORE=		invalid value for WITH_BLAS: ${WITH_BLAS}
 .endif
 
 post-patch:
diff --git a/math/jags/distinfo b/math/jags/distinfo
index e920cdc03af5..40da57aebe54 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,10 +1,10 @@
-SHA256 (mcmc-jags/JAGS-3.4.0.tar.gz) = 2beaa9a2672c2c95efc55ffa4c8b597a872f20232373daebd17ad539d3d7d82b
-SIZE (mcmc-jags/JAGS-3.4.0.tar.gz) = 1677450
+SHA256 (mcmc-jags/JAGS-4.0.0.tar.gz) = a1d572269029d90d4e8b25757fd7ae9678994bd682937ec505ddcf06185d2c4c
+SIZE (mcmc-jags/JAGS-4.0.0.tar.gz) = 1880476
 SHA256 (mcmc-jags/jags_developer_manual.pdf) = 6e7c707b94ffc931807198cc162e8b254859bb774695ae39ef1c1c175560259b
 SIZE (mcmc-jags/jags_developer_manual.pdf) = 71319
-SHA256 (mcmc-jags/jags_installation_manual.pdf) = 4b339af679186783f1bcfc1c31483238cbd46eb9f1f31eb853da51dae61cb3e5
-SIZE (mcmc-jags/jags_installation_manual.pdf) = 167002
-SHA256 (mcmc-jags/jags_user_manual.pdf) = febaf9b22cee57c2fc688a16969d3ddeaa83c1dee7915b872a6cf6772b1f9958
-SIZE (mcmc-jags/jags_user_manual.pdf) = 325886
-SHA256 (mcmc-jags/classic-bugs.tar.gz) = eee97e64f06189a13f6fdee738ea65db088eafa63a5eddedeef66c685f920bae
-SIZE (mcmc-jags/classic-bugs.tar.gz) = 83112
+SHA256 (mcmc-jags/jags_installation_manual.pdf) = 022fcedcf85b259cfe52b13b8a1c3b02a4f0af3ab8370a160c9d5bc739699848
+SIZE (mcmc-jags/jags_installation_manual.pdf) = 208573
+SHA256 (mcmc-jags/jags_user_manual.pdf) = d4151d383868b700531fc54b1b4849085cb313e4e360d72acf031675331383bb
+SIZE (mcmc-jags/jags_user_manual.pdf) = 349318
+SHA256 (mcmc-jags/classic-bugs.tar.gz) = 6428cc0a971010633a349addafcb1c87621557c9497e9fd29cb94bd4e6e04d52
+SIZE (mcmc-jags/classic-bugs.tar.gz) = 83784
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index ba4d4362c1da..ffa76ff6ef2f 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -1,9 +1,7 @@
 bin/mcmc-jags
 include/JAGS/Console.h
 include/JAGS/JRmath.h
-include/JAGS/Module.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
@@ -16,16 +14,25 @@ include/JAGS/distribution/DistError.h
 include/JAGS/distribution/DistPtr.h
 include/JAGS/distribution/DistTab.h
 include/JAGS/distribution/Distribution.h
+include/JAGS/distribution/RScalarDist.h
 include/JAGS/distribution/ScalarDist.h
 include/JAGS/distribution/VectorDist.h
 include/JAGS/function/ArrayFunction.h
+include/JAGS/function/ArrayLogDensity.h
+include/JAGS/function/DFunction.h
+include/JAGS/function/DPQFunction.h
 include/JAGS/function/FuncError.h
 include/JAGS/function/FuncTab.h
 include/JAGS/function/Function.h
 include/JAGS/function/FunctionPtr.h
 include/JAGS/function/LinkFunction.h
+include/JAGS/function/PFunction.h
+include/JAGS/function/QFunction.h
 include/JAGS/function/ScalarFunction.h
+include/JAGS/function/ScalarLogDensity.h
+include/JAGS/function/ScalarVectorFunction.h
 include/JAGS/function/VectorFunction.h
+include/JAGS/function/VectorLogDensity.h
 include/JAGS/graph/AggNode.h
 include/JAGS/graph/ArrayLogicalNode.h
 include/JAGS/graph/ArrayStochasticNode.h
@@ -35,9 +42,11 @@ include/JAGS/graph/Graph.h
 include/JAGS/graph/GraphMarks.h
 include/JAGS/graph/LinkNode.h
 include/JAGS/graph/LogicalNode.h
+include/JAGS/graph/MixTab.h
 include/JAGS/graph/MixtureNode.h
 include/JAGS/graph/Node.h
 include/JAGS/graph/NodeError.h
+include/JAGS/graph/ParentError.h
 include/JAGS/graph/ScalarLogicalNode.h
 include/JAGS/graph/ScalarStochasticNode.h
 include/JAGS/graph/StochasticNode.h
@@ -51,27 +60,34 @@ include/JAGS/model/MonitorControl.h
 include/JAGS/model/MonitorFactory.h
 include/JAGS/model/MonitorInfo.h
 include/JAGS/model/NodeArray.h
+include/JAGS/model/NodeArraySubset.h
 include/JAGS/model/SymTab.h
+include/JAGS/module/Module.h
 include/JAGS/module/ModuleError.h
 include/JAGS/rng/RNG.h
-include/JAGS/rng/RmathRNG.h
 include/JAGS/rng/RNGFactory.h
+include/JAGS/rng/RmathRNG.h
 include/JAGS/rng/TruncatedNormal.h
 include/JAGS/sampler/GraphView.h
+include/JAGS/sampler/ImmutableSampleMethod.h
+include/JAGS/sampler/ImmutableSampler.h
 include/JAGS/sampler/Linear.h
 include/JAGS/sampler/Metropolis.h
-include/JAGS/sampler/ParallelSampler.h
+include/JAGS/sampler/MutableSampleMethod.h
+include/JAGS/sampler/MutableSampler.h
 include/JAGS/sampler/RWMetropolis.h
-include/JAGS/sampler/SampleMethod.h
+include/JAGS/sampler/SampleMethodNoAdapt.h
 include/JAGS/sampler/Sampler.h
 include/JAGS/sampler/SamplerFactory.h
 include/JAGS/sampler/SingletonFactory.h
+include/JAGS/sampler/SingletonGraphView.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
+include/JAGS/sarray/SimpleRange.h
 include/JAGS/util/dim.h
 include/JAGS/util/integer.h
 include/JAGS/util/logical.h
@@ -85,8 +101,8 @@ lib/JAGS/modules-%%MODULEVERSION%%/lecuyer.so
 lib/JAGS/modules-%%MODULEVERSION%%/mix.so
 lib/JAGS/modules-%%MODULEVERSION%%/msm.so
 lib/libjags.so
-lib/libjags.so.3
-lib/libjags.so.3.0.4
+lib/libjags.so.4
+lib/libjags.so.4.0.0
 lib/libjrmath.so
 lib/libjrmath.so.0
 lib/libjrmath.so.0.0.0