ports/146180: [PATCH]math/jags: update to 2.0.0-20100429
bf
bf1783 at gmail.com
Fri Apr 30 09:10:02 UTC 2010
>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 at 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%%
- at dirrm lib/JAGS/modules
+ at dirrm lib/JAGS/modules-2.0.0
@dirrm lib/JAGS
@dirrm include/JAGS/util
@dirrm include/JAGS/sarray
>Release-Note:
>Audit-Trail:
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