update to 3.0.0

5 files changed, 37 insertions, 51 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index 95ea07e0eba4..3d0ea7dada7e 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -7,22 +7,25 @@
 #
 
 PORTNAME=	mcmc-jags
-PORTVERSION=	2.2.0
+PORTVERSION=	3.0.0
 CATEGORIES=	math
-MASTER_SITES=	SF:1,2,3
-MASTER_SITE_SUBDIR=	${PORTNAME}/JAGS/2.x/Source/:1 \
+MASTER_SITES=	SF:1,2,3,4
+MASTER_SITE_SUBDIR=	${PORTNAME}/JAGS/${PORTVERSION:C|\..*|.x|}/Source/:1 \
 		${PORTNAME}/Examples/2.x/:2 \
-		${PORTNAME}/Manuals/2.x/:3
+		${PORTNAME}/Manuals/2.x/:3 \
+		${PORTNAME}/Manuals/${PORTVERSION:C|\..*|.x|}/:4
 DISTFILES=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}:1
 .if !defined(NOPORTDOCS)
 DISTFILES+=	classic-bugs.tar.gz:2 jags_developer_manual.pdf:3 \
-		jags_installation_manual.pdf:3 jags_user_manual.pdf:3
+		jags_installation_manual.pdf:4 jags_user_manual.pdf:4
 EXTRACT_ONLY=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}
 .endif
 
 MAINTAINER=	bf@FreeBSD.org
 COMMENT=	Just Another Gibbs Sampler
 
+LICENSE=	GPLv2
+
 OPTIONS=	ATLAS "use ATLAS libraries instead of BLAS and LAPACK" off
 
 DIST_SUBDIR=	${PORTNAME}
@@ -35,7 +38,7 @@ CONFIGURE_ENV=	LDFLAGS="${LDFLAGS}"
 USE_FORTRAN=	yes
 USE_LDCONFIG=	yes
 USE_BISON=	build
-PLIST_SUB=	PORTVERSION=${PORTVERSION}
+PLIST_SUB=	MODULEVERSION=${PORTVERSION:C|\..*||}
 
 MAN1=		jags.1
 
@@ -64,8 +67,8 @@ post-patch:
 post-install:
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
-.for _M in developer installation user
-	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_${_M}_manual.pdf \
+.for M in developer installation user
+	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_${M}_manual.pdf \
 		${DOCSDIR}
 .endfor
 .endif
diff --git a/math/jags/distinfo b/math/jags/distinfo
index f9051fa35357..ece6d472328c 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,10 +1,10 @@
-SHA256 (mcmc-jags/JAGS-2.2.0.tar.gz) = 6615207cc19463c6398a8c5d02bfc0e3a659928d7da928396f95a63409addd04
-SIZE (mcmc-jags/JAGS-2.2.0.tar.gz) = 1621102
+SHA256 (mcmc-jags/JAGS-3.0.0.tar.gz) = 1cc9a5b1104e2d052a76a8faad2b615a1d9e7f02dd6cd8d514cb6ac9b6b6795e
+SIZE (mcmc-jags/JAGS-3.0.0.tar.gz) = 1610047
 SHA256 (mcmc-jags/classic-bugs.tar.gz) = ae6f9e25f00a3c2bf2d67c8b3fe040f937551ef75407ae0bd8cad5cbc3a8f768
 SIZE (mcmc-jags/classic-bugs.tar.gz) = 81419
 SHA256 (mcmc-jags/jags_developer_manual.pdf) = 6e7c707b94ffc931807198cc162e8b254859bb774695ae39ef1c1c175560259b
 SIZE (mcmc-jags/jags_developer_manual.pdf) = 71319
-SHA256 (mcmc-jags/jags_installation_manual.pdf) = abce36d30b47da443714b08eaec537a97ca5196f2dd5c6ce3816e5b1035125dc
-SIZE (mcmc-jags/jags_installation_manual.pdf) = 118975
-SHA256 (mcmc-jags/jags_user_manual.pdf) = 77d4c2c7160596c34a5d3cec307d66efc44825e965ab43b83ef59fa349999964
-SIZE (mcmc-jags/jags_user_manual.pdf) = 223214
+SHA256 (mcmc-jags/jags_installation_manual.pdf) = 4180b8cac5f05099f54bb93be8084802300d000df20c1b235bebda0c1fc8fc88
+SIZE (mcmc-jags/jags_installation_manual.pdf) = 103315
+SHA256 (mcmc-jags/jags_user_manual.pdf) = 4aedff83e9f4d64c00fc374c16f25c877e97ea0cf407b8b5203cf48f2e943e16
+SIZE (mcmc-jags/jags_user_manual.pdf) = 229343
diff --git a/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc b/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc
deleted file mode 100644
index a34a93edee14..000000000000
--- a/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/modules/bugs/samplers/ConjugateFactory.cc.orig	2011-01-20 05:12:21.000000000 -0500
-+++ src/modules/bugs/samplers/ConjugateFactory.cc	2011-01-20 05:12:46.000000000 -0500
-@@ -120,7 +120,7 @@
- 		method = new ConjugateBeta(gv);
- 	    }
- 	    else {
--		logic_error("Cannot find conjugate sampler for uniform");
-+		throw logic_error("Cannot find conjugate sampler for uniform");
- 	    }
- 	    break;
- 	default:
diff --git a/math/jags/files/patch-src_terminal_parser.yy b/math/jags/files/patch-src_terminal_parser.yy
deleted file mode 100644
index 9a9cbbedee53..000000000000
--- a/math/jags/files/patch-src_terminal_parser.yy
+++ /dev/null
@@ -1,10 +0,0 @@
---- 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 --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index cc554069c416..2b18ec04f079 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -12,12 +12,14 @@ 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/ScalarDist.h
 include/JAGS/distribution/VectorDist.h
 include/JAGS/function/ArrayFunction.h
+include/JAGS/function/FuncError.h
 include/JAGS/function/FuncTab.h
 include/JAGS/function/Function.h
 include/JAGS/function/FunctionPtr.h
@@ -50,6 +52,7 @@ include/JAGS/model/MonitorFactory.h
 include/JAGS/model/MonitorInfo.h
 include/JAGS/model/NodeArray.h
 include/JAGS/model/SymTab.h
+include/JAGS/module/ModuleError.h
 include/JAGS/rng/RNG.h
 include/JAGS/rng/RmathRNG.h
 include/JAGS/rng/RNGFactory.h
@@ -74,23 +77,23 @@ include/JAGS/util/integer.h
 include/JAGS/util/logical.h
 include/JAGS/util/nainf.h
 include/JAGS/version.h
-lib/JAGS/modules-%%PORTVERSION%%/basemod.la
-lib/JAGS/modules-%%PORTVERSION%%/basemod.so
-lib/JAGS/modules-%%PORTVERSION%%/bugs.la
-lib/JAGS/modules-%%PORTVERSION%%/bugs.so
-lib/JAGS/modules-%%PORTVERSION%%/dic.la
-lib/JAGS/modules-%%PORTVERSION%%/dic.so
-lib/JAGS/modules-%%PORTVERSION%%/glm.la
-lib/JAGS/modules-%%PORTVERSION%%/glm.so
-lib/JAGS/modules-%%PORTVERSION%%/lecuyer.la
-lib/JAGS/modules-%%PORTVERSION%%/lecuyer.so
-lib/JAGS/modules-%%PORTVERSION%%/mix.la
-lib/JAGS/modules-%%PORTVERSION%%/mix.so
-lib/JAGS/modules-%%PORTVERSION%%/msm.la
-lib/JAGS/modules-%%PORTVERSION%%/msm.so
+lib/JAGS/modules-%%MODULEVERSION%%/basemod.la
+lib/JAGS/modules-%%MODULEVERSION%%/basemod.so
+lib/JAGS/modules-%%MODULEVERSION%%/bugs.la
+lib/JAGS/modules-%%MODULEVERSION%%/bugs.so
+lib/JAGS/modules-%%MODULEVERSION%%/dic.la
+lib/JAGS/modules-%%MODULEVERSION%%/dic.so
+lib/JAGS/modules-%%MODULEVERSION%%/glm.la
+lib/JAGS/modules-%%MODULEVERSION%%/glm.so
+lib/JAGS/modules-%%MODULEVERSION%%/lecuyer.la
+lib/JAGS/modules-%%MODULEVERSION%%/lecuyer.so
+lib/JAGS/modules-%%MODULEVERSION%%/mix.la
+lib/JAGS/modules-%%MODULEVERSION%%/mix.so
+lib/JAGS/modules-%%MODULEVERSION%%/msm.la
+lib/JAGS/modules-%%MODULEVERSION%%/msm.so
 lib/libjags.la
 lib/libjags.so
-lib/libjags.so.2
+lib/libjags.so.3
 lib/libjrmath.la
 lib/libjrmath.so
 lib/libjrmath.so.0
@@ -457,12 +460,13 @@ libexec/jags-terminal
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/R
 %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm lib/JAGS/modules-%%PORTVERSION%%
+@dirrm lib/JAGS/modules-%%MODULEVERSION%%
 @dirrm lib/JAGS
 @dirrm include/JAGS/util
 @dirrm include/JAGS/sarray
 @dirrm include/JAGS/sampler
 @dirrm include/JAGS/rng
+@dirrm include/JAGS/module
 @dirrm include/JAGS/model
 @dirrm include/JAGS/graph
 @dirrm include/JAGS/function