Date: Fri, 30 Apr 2010 09:09:21 GMT From: bf <bf1783@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/146180: [PATCH]math/jags: update to 2.0.0-20100429 Message-ID: <201004300909.o3U99LnD084396@www.freebsd.org> Resent-Message-ID: <201004300910.o3U9A2E2018550@freefall.freebsd.org>
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>Number: 146180 >Category: ports >Synopsis: [PATCH]math/jags: update to 2.0.0-20100429 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Fri Apr 30 09:10:02 UTC 2010 >Closed-Date: >Last-Modified: >Originator: bf >Release: 9-CURRENT amd64 >Organization: - >Environment: >Description: >How-To-Repeat: >Fix: Patch attached with submission follows: diff -x '*old.*' -x '*new.*' -ruN jags.orig/Makefile jags/Makefile --- jags.orig/Makefile 2010-04-29 23:29:26.000000000 -0400 +++ jags/Makefile 2010-04-30 04:48:57.000000000 -0400 @@ -7,21 +7,22 @@ # PORTNAME= jags -PORTVERSION= 1.0.4 -PORTREVISION= 1 +DISTVERSION= 2.0.0-20100429 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= mcmc-jags/JAGS/2.0/Source/:1 \ + mcmc-jags/Examples/2.0/:2 \ + mcmc-jags/Manuals/2.0/:3 +DISTFILES= ${DISTNAME:U}${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= ${DISTNAME:U}${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 @@ -32,9 +33,11 @@ .endif DIST_SUBDIR= ${PORTNAME} +WRKSRC= ${WRKDIR}/${PKGNAME:U:R} GNU_CONFIGURE= yes -CONFIGURE_ENV= LDFLAGS=-L${LOCALBASE}/lib +LDFLAGS+= -L${LOCALBASE}/lib +CONFIGURE_ENV= LDFLAGS="${LDFLAGS}" USE_FORTRAN= yes USE_LDCONFIG= yes @@ -45,8 +48,10 @@ 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} diff -x '*old.*' -x '*new.*' -ruN jags.orig/distinfo jags/distinfo --- jags.orig/distinfo 2010-04-29 23:29:26.000000000 -0400 +++ jags/distinfo 2010-04-29 23:48:32.000000000 -0400 @@ -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 (jags/JAGS-2.0.0-20100429.tar.gz) = 492971b4983a64ed19426ef2a199a3a3 +SHA256 (jags/JAGS-2.0.0-20100429.tar.gz) = 5eb80ae180cb1a9f130e70b43948398560e827addb159a76c146ccf9d7ede9e6 +SIZE (jags/JAGS-2.0.0-20100429.tar.gz) = 1169463 +MD5 (jags/classic-bugs.tar.gz) = 7df4366dfb5278cbd4ce43f21b4d9e6c +SHA256 (jags/classic-bugs.tar.gz) = 3814414bb5d23b1757f85cea549561389cf6d514cecad9a9ef945e21f806c3af +SIZE (jags/classic-bugs.tar.gz) = 81193 +MD5 (jags/jags_developer_manual.pdf) = 850864bef54ff17858f8bf341b0c13c1 +SHA256 (jags/jags_developer_manual.pdf) = 09d06b202adcbc9a52bd889c19c741ffb13f68b6657b9a0a999ad3f89259eb19 +SIZE (jags/jags_developer_manual.pdf) = 71199 +MD5 (jags/jags_installation_manual.pdf) = ad203ece5acdabcade940d0475ea17d8 +SHA256 (jags/jags_installation_manual.pdf) = 86f5c9acd1efc8b5088114f93ba64d43af5d77436553594e5d331556b544a7cd +SIZE (jags/jags_installation_manual.pdf) = 119269 +MD5 (jags/jags_user_manual.pdf) = efe47f0332544809627f57c209ca2068 +SHA256 (jags/jags_user_manual.pdf) = 39f642e407a03c2e335adef5fca6af09ae5f9af312274dbb535b652c183b1aff +SIZE (jags/jags_user_manual.pdf) = 221001 diff -x '*old.*' -x '*new.*' -ruN jags.orig/files/patch-src_terminal_parser.yy jags/files/patch-src_terminal_parser.yy --- jags.orig/files/patch-src_terminal_parser.yy 1969-12-31 19:00:00.000000000 -0500 +++ jags/files/patch-src_terminal_parser.yy 2010-04-30 03:24:20.000000000 -0400 @@ -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 -x '*old.*' -x '*new.*' -ruN jags.orig/pkg-plist jags/pkg-plist --- jags.orig/pkg-plist 2010-04-29 23:29:26.000000000 -0400 +++ jags/pkg-plist 2010-04-30 03:14:20.000000000 -0400 @@ -9,44 +9,63 @@ 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/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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 @@ %%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 >Release-Note: >Audit-Trail: >Unformatted:
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