Index: head/math/jags/Makefile =================================================================== --- head/math/jags/Makefile (revision 405179) +++ head/math/jags/Makefile (revision 405180) @@ -1,100 +1,98 @@ # Created by: Eric van Gyzen # $FreeBSD$ 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 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|\..*||} OPTIONS_DEFINE= DOCS EXAMPLES .include .if ${PORT_OPTIONS:MDOCS} || make(makesum) DISTFILES+= jags_developer_manual.pdf:3 jags_installation_manual.pdf:4 \ jags_user_manual.pdf:4 PORTDOCS= ${DISTFILES:M*[34]:C|:.*||} .endif .if ${PORT_OPTIONS:MEXAMPLES} || make(makesum) DISTFILES+= classic-bugs.tar.gz:2 PORTEXAMPLES= * .endif .if exists(${LOCALBASE}/lib/libatlas.so) WITH_BLAS?= atlas .else WITH_BLAS?= reference .endif .if ${WITH_BLAS} == "atlas" LIB_DEPENDS+= libatlas.so:${PORTSDIR}/math/atlas CONFIGURE_ARGS= --with-lapack="-lalapack -lptcblas" --with-blas="-lptf77blas" .elif ${WITH_BLAS} == "reference" LIB_DEPENDS+= libblas.so:${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: ${WITH_BLAS} .endif post-patch: @${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 .if ${PORT_OPTIONS:MEXAMPLES} @${SED} -i '' -e '\|JAGS ?=|{s|jags|mcmc-&|;s|/usr/local|${PREFIX}|;}' \ ${WRKDIR}/classic-bugs/vol[12]/Makefile .endif post-install: .if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${STAGEDIR}${DOCSDIR} @cd ${_DISTDIR}; ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR} .endif .if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} @cd ${WRKDIR}/classic-bugs; ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR} .endif .if defined(MAINTAINER_MODE) BUILD_DEPENDS+= ${LOCALBASE}/lib/R/library/coda/R/coda.rdb:${PORTSDIR}/math/R-cran-coda check test: install .for i in 1 2 @cd ${WRKDIR}/classic-bugs/vol${i}; ${SETENV} ${MAKE_ENV} \ ${MAKE_CMD} ${MAKE_ARGS} check .endfor @${FIND} ${WRKDIR}/classic-bugs -type f -name check.log | ${SORT} | \ ${XARGS} -tI @ ${CAT} @ .endif .include Index: head/math/jags/distinfo =================================================================== --- head/math/jags/distinfo (revision 405179) +++ head/math/jags/distinfo (revision 405180) @@ -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 Index: head/math/jags/pkg-plist =================================================================== --- head/math/jags/pkg-plist (revision 405179) +++ head/math/jags/pkg-plist (revision 405180) @@ -1,95 +1,111 @@ 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 include/JAGS/compiler/MixtureFactory.h include/JAGS/compiler/NodeFactory.h include/JAGS/compiler/ObsFuncTab.h include/JAGS/compiler/ParseTree.h include/JAGS/distribution/ArrayDist.h 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 include/JAGS/graph/ConstantNode.h include/JAGS/graph/DeterministicNode.h 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 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/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 include/JAGS/util/nainf.h include/JAGS/version.h lib/JAGS/modules-%%MODULEVERSION%%/basemod.so lib/JAGS/modules-%%MODULEVERSION%%/bugs.so lib/JAGS/modules-%%MODULEVERSION%%/dic.so lib/JAGS/modules-%%MODULEVERSION%%/glm.so 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 libdata/pkgconfig/jags.pc libexec/jags-terminal man/man1/jags.1.gz