Update to 2.2.0

PR:		154053
Submitted by:	wen
Approved by:	makc, miwi (mentors, implicit)
Feature safe:	yes

6 files changed, 42 insertions, 42 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index d990de6941b7..2c35fa9df6b3 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -7,12 +7,12 @@
 #
 
 PORTNAME=	mcmc-jags
-PORTVERSION=	2.1.0
+PORTVERSION=	2.2.0
 CATEGORIES=	math
 MASTER_SITES=	SF:1,2,3
 MASTER_SITE_SUBDIR=	${PORTNAME}/JAGS/2.x/Source/:1 \
-		${PORTNAME}/Examples/2.0/:2 \
-		${PORTNAME}/Manuals/2.0/:3
+		${PORTNAME}/Examples/2.x/:2 \
+		${PORTNAME}/Manuals/2.x/:3
 DISTFILES=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}:1
 .if !defined(NOPORTDOCS)
 DISTFILES+=	classic-bugs.tar.gz:2 jags_developer_manual.pdf:3 \
@@ -37,6 +37,8 @@ USE_LDCONFIG=	yes
 USE_BISON=	build
 PLIST_SUB=	PORTVERSION=${PORTVERSION}
 
+MAN1=		jags.1
+
 .include <bsd.port.options.mk>
 
 .if defined(WITH_ATLAS)
@@ -73,12 +75,24 @@ post-install:
 	  ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/classic-bugs.tar.gz \
 	    -s ':^classic-bugs/*::' )
 	${SED} -i '' \
-		-e '\|JAGS ?=|{s|/usr/local|${PREFIX}|;s|jags|mcmc-&|;}' \
+		-e '\|JAGS ?=|{s|jags|mcmc-&|;s|/usr/local|${PREFIX}|;}' \
 		${EXAMPLESDIR}/vol[12]/Makefile
+	${SED} -i '' -e '\|EXAMPLES ?=|{s|litters||;}' \
+		${EXAMPLESDIR}/vol1/Makefile
 	@${ECHO_MSG} ""
 	@${CAT} ${PKGMESSAGE}
 	@${ECHO_MSG} ""
 
 .endif
 
+.if defined(MAINTAINER_MODE)
+RUN_DEPENDS+=	${LOCALBASE}/lib/R/library/coda/R/coda.rdb:${PORTSDIR}/math/R-cran-coda
+
+regression-test test check:	install
+.for _i in 1 2
+	 ( cd ${EXAMPLESDIR}/vol${_i} && ${SETENV} ${MAKE_ENV} ${MAKE} \
+	 	${_MAKE_JOBS} ${MAKE_ARGS} clean check clean)
+.endfor
+
+.endif
 .include <bsd.port.mk>
diff --git a/math/jags/distinfo b/math/jags/distinfo
index a50009f56a71..f6cd2ba6ee6b 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,15 +1,10 @@
-MD5 (mcmc-jags/JAGS-2.1.0.tar.gz) = ddb5eb745cb48537517aba186d7030c8
-SHA256 (mcmc-jags/JAGS-2.1.0.tar.gz) = c713a7f1856f2153a94e96bdf26d1e2dff4e3dc9156864d6798d6b3b157d6e68
-SIZE (mcmc-jags/JAGS-2.1.0.tar.gz) = 1171371
-MD5 (mcmc-jags/classic-bugs.tar.gz) = 98d32deaaf134ade265c0a6146291796
-SHA256 (mcmc-jags/classic-bugs.tar.gz) = 3e4902c08c7823a948fba4d7dc32f5140e56c59f170b12e63ac7f4ffc4a7f8cc
-SIZE (mcmc-jags/classic-bugs.tar.gz) = 81313
-MD5 (mcmc-jags/jags_developer_manual.pdf) = 850864bef54ff17858f8bf341b0c13c1
-SHA256 (mcmc-jags/jags_developer_manual.pdf) = 09d06b202adcbc9a52bd889c19c741ffb13f68b6657b9a0a999ad3f89259eb19
-SIZE (mcmc-jags/jags_developer_manual.pdf) = 71199
-MD5 (mcmc-jags/jags_installation_manual.pdf) = 42a78397a85100d2cfbde4c92aad3b9f
-SHA256 (mcmc-jags/jags_installation_manual.pdf) = d7147c7a57a1e55305c48bcbefbffd19090e958cc55339160c46401fa1d5955a
-SIZE (mcmc-jags/jags_installation_manual.pdf) = 119855
-MD5 (mcmc-jags/jags_user_manual.pdf) = efe47f0332544809627f57c209ca2068
+SHA256 (mcmc-jags/JAGS-2.2.0.tar.gz) = 6615207cc19463c6398a8c5d02bfc0e3a659928d7da928396f95a63409addd04
+SIZE (mcmc-jags/JAGS-2.2.0.tar.gz) = 1621102
+SHA256 (mcmc-jags/classic-bugs.tar.gz) = 1ab4a8f4d6e8765230b00bb8969c8b5375b3f9c1bf57c2d50b89287fbbc52205
+SIZE (mcmc-jags/classic-bugs.tar.gz) = 81419
+SHA256 (mcmc-jags/jags_developer_manual.pdf) = 606f3923fe2f2a45d9a2ca3d284009864ee8ce2906858897330564697fc8e2cb
+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) = 39f642e407a03c2e335adef5fca6af09ae5f9af312274dbb535b652c183b1aff
 SIZE (mcmc-jags/jags_user_manual.pdf) = 221001
diff --git a/math/jags/files/patch-src__modules__bugs__matrix__matrix.cc b/math/jags/files/patch-src__modules__bugs__matrix__matrix.cc
deleted file mode 100644
index fb5ee245cd9d..000000000000
--- a/math/jags/files/patch-src__modules__bugs__matrix__matrix.cc
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/modules/bugs/matrix/matrix.cc.orig	2009-12-26 15:49:36.000000000 -0500
-+++ src/modules/bugs/matrix/matrix.cc	2009-12-26 15:48:07.000000000 -0500
-@@ -41,6 +41,7 @@
-   }
- 
-   if (w[0] <= 0) {
-+    delete [] w;
-     throw runtime_error("Non positive definite matrix in call to logdet");
-   }
- 
diff --git a/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc b/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc
new file mode 100644
index 000000000000..a34a93edee14
--- /dev/null
+++ b/math/jags/files/patch-src__modules__bugs__samplers__ConjugateFactory.cc
@@ -0,0 +1,11 @@
+--- 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__modules__msm__matrix__matexp.cc b/math/jags/files/patch-src__modules__msm__matrix__matexp.cc
deleted file mode 100644
index eff874cf76d3..000000000000
--- a/math/jags/files/patch-src__modules__msm__matrix__matexp.cc
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/modules/msm/matrix/matexp.cc.orig	2009-12-26 15:36:17.000000000 -0500
-+++ src/modules/msm/matrix/matexp.cc	2009-12-26 15:36:54.000000000 -0500
-@@ -73,6 +73,8 @@
-     int info = 0;
-     F77_DGESV (&n, &n, Acopy, &n, ipiv, X, &n, &info);
-     if (info != 0) {
-+	delete [] Acopy;
-+	delete [] ipiv;
- 	throw runtime_error("Unable to solve linear equations");
-     }
-   
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index 8ad17a568e2c..cc554069c416 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -15,11 +15,7 @@ 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
@@ -54,6 +50,10 @@ include/JAGS/model/MonitorFactory.h
 include/JAGS/model/MonitorInfo.h
 include/JAGS/model/NodeArray.h
 include/JAGS/model/SymTab.h
+include/JAGS/rng/RNG.h
+include/JAGS/rng/RmathRNG.h
+include/JAGS/rng/RNGFactory.h
+include/JAGS/rng/TruncatedNormal.h
 include/JAGS/sampler/GraphView.h
 include/JAGS/sampler/Linear.h
 include/JAGS/sampler/Metropolis.h
@@ -462,6 +462,7 @@ libexec/jags-terminal
 @dirrm include/JAGS/util
 @dirrm include/JAGS/sarray
 @dirrm include/JAGS/sampler
+@dirrm include/JAGS/rng
 @dirrm include/JAGS/model
 @dirrm include/JAGS/graph
 @dirrm include/JAGS/function