git: f80dfca614bb - main - math/jags: upgrade to 5.0.0

Thierry Thomas <[email protected]>
Newsgroups gmane.os.freebsd.devel.cvs.ports
Message-ID <[email protected]> 
The branch main has been updated by thierry:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f80dfca614bb4e66163363ea8f6a58524baa94f8

commit f80dfca614bb4e66163363ea8f6a58524baa94f8
Author:     Thierry Thomas <[email protected]>
AuthorDate: 2026-08-13 16:02:00 +0000
Commit:     Thierry Thomas <[email protected]>
CommitDate: 2026-08-13 16:06:10 +0000

    math/jags: upgrade to 5.0.0
    
    News at
    https://martynplummer.wordpress.com/2026/08/03/whats-new-in-jags-5-0-0-part-1-initial-values/
    https://martynplummer.wordpress.com/2026/08/04/whats-new-in-jags-5-0-0-part-2-reproducibility/
---
 math/jags/Makefile  | 13 +++++--------
 math/jags/distinfo  | 14 +++++++-------
 math/jags/pkg-plist | 23 +++++++++++++++++++----
 3 files changed, 31 insertions(+), 19 deletions(-)

diff --git a/math/jags/Makefile b/math/jags/Makefile
index 31d021c7c0b4..ee8b876c769b 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -1,9 +1,9 @@
 PORTNAME=	mcmc-jags
-DISTVERSION=	4.3.2
+DISTVERSION=	5.0.0
 CATEGORIES=	math
 MASTER_SITES=	SF/mcmc-jags/JAGS/${S}.x/Source/:1 \
-		SF/mcmc-jags/Examples/${S}.x/:2 \
-		SF/mcmc-jags/Manuals/2.x/:3 \
+		SF/mcmc-jags/Examples/4.x/:2 \
+		SF/mcmc-jags/Manuals/5.x/:3 \
 		SF/mcmc-jags/Manuals/${S}.x/:4
 DISTFILES=	JAGS-${PORTVERSION}${EXTRACT_SUFX}:1
 DIST_SUBDIR=	${PORTNAME}
@@ -18,6 +18,7 @@ LICENSE_FILE=	${WRKSRC}/COPYING
 
 BUILD_DEPENDS=	cppunit>0:devel/cppunit
 LIB_DEPENDS=	libltdl.so:devel/libltdl
+TEST_DEPENDS+=	${LOCALBASE}/lib/R/library/coda/R/coda.rdb:math/R-cran-coda
 
 USES=		bison compiler:features fortran gmake libtool localbase pathfix pkgconfig
 
@@ -71,10 +72,7 @@ post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	cd ${WRKDIR}/classic-bugs; ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR}
 
-.if defined(MAINTAINER_MODE)
-BUILD_DEPENDS+=	${LOCALBASE}/lib/R/library/coda/R/coda.rdb:math/R-cran-coda
-
-check test: install
+test: install
 .for i in 1 2
 	@cd ${WRKDIR}/classic-bugs/vol${i}; ${SETENV} ${MAKE_ENV} \
 	${MAKE_CMD} ${MAKE_ARGS} check
@@ -82,5 +80,4 @@ check test: install
 	@${FIND} ${WRKDIR}/classic-bugs -type f -name check.log | ${SORT} | \
 	${XARGS} -tI @  ${CAT} @
 
-.endif
 .include <bsd.port.mk>
diff --git a/math/jags/distinfo b/math/jags/distinfo
index dbd029cf040b..80f24c22c29f 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,11 +1,11 @@
-TIMESTAMP = 1782408725
-SHA256 (mcmc-jags/JAGS-4.3.2.tar.gz) = 871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8
-SIZE (mcmc-jags/JAGS-4.3.2.tar.gz) = 2032834
+TIMESTAMP = 1786631696
+SHA256 (mcmc-jags/JAGS-5.0.0.tar.gz) = 64fcd4883b8a8ee907722f49366cc9f277477a0647ada61356f17568f84ffff8
+SIZE (mcmc-jags/JAGS-5.0.0.tar.gz) = 2158256
 SHA256 (mcmc-jags/jags_developer_manual.pdf) = 6e7c707b94ffc931807198cc162e8b254859bb774695ae39ef1c1c175560259b
 SIZE (mcmc-jags/jags_developer_manual.pdf) = 71319
-SHA256 (mcmc-jags/jags_installation_manual.pdf) = 836b31f3fef4335c6dad04339c90a7542e60743d4a6087cf356f2a3d60521474
-SIZE (mcmc-jags/jags_installation_manual.pdf) = 214355
-SHA256 (mcmc-jags/jags_user_manual.pdf) = d73a023dc87654e6ae56eb27cc6dba25097e00ddd2d8f7ca2639f27d55e581a3
-SIZE (mcmc-jags/jags_user_manual.pdf) = 429729
+SHA256 (mcmc-jags/jags_installation_manual.pdf) = 09bba065a1d2d2c902e17a6c867cfa46748fb1b218509ada52892d6578cdcf98
+SIZE (mcmc-jags/jags_installation_manual.pdf) = 174873
+SHA256 (mcmc-jags/jags_user_manual.pdf) = 62b82131398c223fd50d8e9b0919f5731676462528db01662bd1d6c0ca52651d
+SIZE (mcmc-jags/jags_user_manual.pdf) = 520227
 SHA256 (mcmc-jags/classic-bugs.tar.gz) = cbecdd184516ed1e0ed26993335c7ce6b50b85875c66a059a4ad51780547e580
 SIZE (mcmc-jags/classic-bugs.tar.gz) = 86183
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index ae0b8eeb65bc..e2d891fa562d 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -5,7 +5,6 @@ include/JAGS/compiler/Compiler.h
 include/JAGS/compiler/Counter.h
 include/JAGS/compiler/CounterTab.h
 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
@@ -44,24 +43,37 @@ include/JAGS/graph/LinkNode.h
 include/JAGS/graph/LogicalNode.h
 include/JAGS/graph/MixTab.h
 include/JAGS/graph/MixtureNode.h
+include/JAGS/graph/MixtureNodeError.h
 include/JAGS/graph/Node.h
 include/JAGS/graph/NodeError.h
-include/JAGS/graph/ParentError.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/matrix/blas.h
+include/JAGS/matrix/lapack.h
+include/JAGS/matrix/matrix.h
 include/JAGS/model/BUGSModel.h
+include/JAGS/model/CovMonitor.h
+include/JAGS/model/ESSWeight.h
+include/JAGS/model/MeanMonitor.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/MonitorStat.h
 include/JAGS/model/NodeArray.h
 include/JAGS/model/NodeArraySubset.h
+include/JAGS/model/StochasticIndex.h
 include/JAGS/model/SymTab.h
+include/JAGS/model/TraceMonitor.h
+include/JAGS/model/TraceWeight.h
+include/JAGS/model/VarMonitor.h
+include/JAGS/model/WeightMonitor.h
+include/JAGS/model/WeightedTraceMonitor.h
 include/JAGS/module/Module.h
 include/JAGS/module/ModuleError.h
 include/JAGS/rng/RNG.h
@@ -88,21 +100,24 @@ include/JAGS/sarray/Range.h
 include/JAGS/sarray/RangeIterator.h
 include/JAGS/sarray/SArray.h
 include/JAGS/sarray/SimpleRange.h
+include/JAGS/util/Factory.h
 include/JAGS/util/dim.h
 include/JAGS/util/integer.h
 include/JAGS/util/logical.h
 include/JAGS/util/nainf.h
+include/JAGS/util/parallel.h
 include/JAGS/version.h
 lib/JAGS/modules-%%MODULEVERSION%%/basemod.so
 lib/JAGS/modules-%%MODULEVERSION%%/bugs.so
+lib/JAGS/modules-%%MODULEVERSION%%/diag.so
 lib/JAGS/modules-%%MODULEVERSION%%/dic.so
 lib/JAGS/modules-%%MODULEVERSION%%/glm.so
 lib/JAGS/modules-%%MODULEVERSION%%/lecuyer.so
 lib/JAGS/modules-%%MODULEVERSION%%/mix.so
 lib/JAGS/modules-%%MODULEVERSION%%/msm.so
 lib/libjags.so
-lib/libjags.so.4
-lib/libjags.so.4.0.3
+lib/libjags.so.5
+lib/libjags.so.5.0.0
 lib/libjrmath.so
 lib/libjrmath.so.0
 lib/libjrmath.so.0.0.0
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