Attachment 105674 Details for Bug 146180 – file.diff

[patch] file.diff

file.diff (text/plain), 11.06 KB, created by bf on 2010-04-30 10:10:02 UTC

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Creator: bf

Created: 2010-04-30 10:10:02 UTC

Size: 11.06 KB

patch

obsolete

>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

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Attachments on bug 146180: 105674