update to 3.2.0, simplify, and fix NOPORTEXAMPLES

3 files changed, 47 insertions, 408 deletions

diff --git a/math/jags/Makefile b/math/jags/Makefile
index e3b78d0ac07e..4795628e6c3b 100644
--- a/math/jags/Makefile
+++ b/math/jags/Makefile
@@ -7,49 +7,60 @@
 #
 
 PORTNAME=	mcmc-jags
-PORTVERSION=	3.1.0
+PORTVERSION=	3.2.0
 CATEGORIES=	math
 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 \
-		${PORTNAME}/Manuals/${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:4 jags_user_manual.pdf:4
-EXTRACT_ONLY=	${DISTNAME:S/mcmc-//:U}${EXTRACT_SUFX}
+MASTER_SITE_SUBDIR=	mcmc-jags/JAGS/${S}.x/Source/:1 \
+		mcmc-jags/Examples/2.x/:2 \
+		mcmc-jags/Manuals/2.x/:3 \
+		mcmc-jags/Manuals/${S}.x/:4
+DISTFILES=	JAGS-${PORTVERSION}${EXTRACT_SUFX}:1
+.if !defined(NOPORTDOCS) || make(makesum)
+DISTFILES+=	jags_developer_manual.pdf:3 jags_installation_manual.pdf:4 \
+		jags_user_manual.pdf:4
+.endif
+.if !defined(NOPORTEXAMPLES) || make(makesum)
+DISTFILES+=	classic-bugs.tar.gz:2
 .endif
+EXTRACT_ONLY=	${DISTFILES:M*[12]:C|:.*||}
 
 MAINTAINER=	bf@FreeBSD.org
 COMMENT=	Just Another Gibbs Sampler
 
 LICENSE=	GPLv2
 
-OPTIONS=	ATLAS "use ATLAS libraries instead of BLAS and LAPACK" off
+GNU_CONFIGURE=	yes
+USE_BISON=	build
+USE_FORTRAN=	yes
+USE_LDCONFIG=	yes
 
 DIST_SUBDIR=	${PORTNAME}
-WRKSRC=		${WRKDIR}/${PKGNAME:S/mcmc-//:U}
+WRKSRC=		${WRKDIR}/JAGS-${PORTVERSION}
 
-GNU_CONFIGURE=	yes
 CPPFLAGS+=	-I${LOCALBASE}/include
 LDFLAGS+=	-L${LOCALBASE}/lib
-USE_FORTRAN=	yes
-USE_LDCONFIG=	yes
-USE_BISON=	build
-PLIST_SUB=	MODULEVERSION=${PORTVERSION:C|\..*||}
-
 MAN1=		jags.1
+OPTIONS=	ATLAS "use ATLAS libraries instead of BLAS and LAPACK" off
+PLIST_SUB=	MODULEVERSION=${S}
+S=		${PORTVERSION:C|\..*||}
 
 .include <bsd.port.options.mk>
 
 .if defined(WITH_ATLAS)
 LIB_DEPENDS+=	atlas.2:${PORTSDIR}/math/atlas
-CONFIGURE_ARGS=	--with-lapack="-lalapack -lcblas" --with-blas=-lf77blas
+CONFIGURE_ARGS=	--with-lapack="-lalapack -lptcblas" --with-blas="-lptf77blas"
 .else
 LIB_DEPENDS+=	blas.2:${PORTSDIR}/math/blas
 LIB_DEPENDS+=	lapack.4:${PORTSDIR}/math/lapack
-CONFIGURE_ARGS=	--with-lapack=-llapack --with-blas=-lblas
+CONFIGURE_ARGS=	--with-lapack="-llapack" --with-blas="-lblas"
+.endif
+
+.if !defined(NOPORTDOCS)
+PORTDOCS=	${DISTFILES:M*[34]:C|:.*||}
+.endif
+
+.if !defined(NOPORTEXAMPLES)
+PORTEXAMPLES=	*
 .endif
 
 post-patch:
@@ -62,42 +73,31 @@ post-patch:
 		-e '/@WINDOWS_FALSE@.*rm -f jags/s/jags/mcmc-&/' \
 		-e '/@WINDOWS_FALSE@.*mv jags.tmp jags/s/jags/mcmc-&/2' \
 		${WRKSRC}/src/terminal/Makefile.in
+.if !defined(NOPORTEXAMPLES)
+	@${SED} -i '' -e '\|JAGS ?=|{s|jags|mcmc-&|;s|/usr/local|${PREFIX}|;}' \
+		${WRKDIR}/classic-bugs/vol[12]/Makefile
+.endif
 
 post-install:
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
-.for M in developer installation user
-	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/jags_${M}_manual.pdf \
-		${DOCSDIR}
-.endfor
+	@cd ${_DISTDIR}; ${INSTALL_DATA} ${PORTDOCS} ${DOCSDIR}
 .endif
 .if !defined(NOPORTEXAMPLES)
 	@${MKDIR} ${EXAMPLESDIR}
-	@( cd ${EXAMPLESDIR}; \
-	  ${PAX} -rzf ${DISTDIR}/${DIST_SUBDIR}/classic-bugs.tar.gz \
-	    -s ':^classic-bugs/*::' )
-	@${SED} -i '' \
-		-e '\|JAGS ?=|{s|jags|mcmc-&|;s|/usr/local|${PREFIX}|;}' \
-		${EXAMPLESDIR}/vol[12]/Makefile
+	@cd ${WRKDIR}/classic-bugs; ${COPYTREE_SHARE} \* ${EXAMPLESDIR}
+.endif
 	@${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
-
-testclean:	install
-.for _i in 1 2
-	@( cd ${EXAMPLESDIR}/vol${_i} && ${SETENV} ${MAKE_ENV} ${MAKE} \
-	 	${_MAKE_JOBS} ${MAKE_ARGS} clean)
-.endfor
+BUILD_DEPENDS+=	${LOCALBASE}/lib/R/library/coda/R/coda.rdb:${PORTSDIR}/math/R-cran-coda
 
-regression-test test check:	testclean
-.for _i in 1 2
-	@( cd ${EXAMPLESDIR}/vol${_i} && ${SETENV} ${MAKE_ENV} ${MAKE} \
-	 	${_MAKE_JOBS} ${MAKE_ARGS} check)
+check test: install
+.for i in 1 2
+	cd ${WRKDIR}/classic-bugs/vol${i}; ${SETENV} ${MAKE_ENV} \
+	${MAKE} ${_MAKE_JOBS} ${MAKE_ARGS} check
 .endfor
 
 .endif
diff --git a/math/jags/distinfo b/math/jags/distinfo
index e8e2c8014ed5..5967b70aa1b3 100644
--- a/math/jags/distinfo
+++ b/math/jags/distinfo
@@ -1,10 +1,10 @@
-SHA256 (mcmc-jags/JAGS-3.1.0.tar.gz) = 69ece562dbd09ad4b493ec0576e9951faf4e16e0ae78302752ef199dff3c4e0b
-SIZE (mcmc-jags/JAGS-3.1.0.tar.gz) = 1609007
+SHA256 (mcmc-jags/JAGS-3.2.0.tar.gz) = 0c8060baf2b8d2e0687b23c190fa88bbbf0fbf0e66d53ef24832fd5c4a486dcf
+SIZE (mcmc-jags/JAGS-3.2.0.tar.gz) = 1625178
 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) = 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
+SHA256 (mcmc-jags/jags_user_manual.pdf) = 1a82401d2283134c10f653430858ccd2f958f3c770a30d97640ccad0831e08a6
+SIZE (mcmc-jags/jags_user_manual.pdf) = 269033
diff --git a/math/jags/pkg-plist b/math/jags/pkg-plist
index 2b18ec04f079..e7a048f902c1 100644
--- a/math/jags/pkg-plist
+++ b/math/jags/pkg-plist
@@ -99,367 +99,6 @@ 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
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/R/check.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/bench-test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blocker-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blocker-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blocker.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blockert-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blockert.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blockht-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/blockht.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/notest2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/notest3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/blocker/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/bones-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/bones-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/bones.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/bones/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/dyes-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/dyes-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/dyes.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/dyes/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/epil/bench-test2.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/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
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/equiv-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/equiv-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/equiv.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/equivmiss-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/equiv/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/inhaler.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/inhaler/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/kidney.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/kidney/notest1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk-poisson.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk-s.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leuk.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leukfr-s.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/leukfr.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/leuk/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/line-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/line-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/line.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/line/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/litters-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/litters-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/litters.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/litters/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat2-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/lsat2.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/lsat/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/mice-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/mice-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/mice.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/mice/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/oxford-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/oxford-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/oxford.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/oxford.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/oxford/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/pump-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/pump-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/pump.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/pump/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/rats-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/rats-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/rats.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/ratsmiss-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/rats/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/salm-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/salm-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/salm-pareto.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/salm.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/salm/test1.R
-%%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/seeds-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seeds-init.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seeds.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/seedspar.bug
-%%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
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test4.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test5.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol1/seeds/test5.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/air-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/air-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/air.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/bench.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/air/notest1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/alli-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/alli-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/alli.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/alli/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/asia-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/asia.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/asia2-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/asia2.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/asia/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/beetles-cloglog.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/beetles-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/beetles-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/beetles-logit.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/beetles-probit.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/bench-test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/beetles/test3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/biops-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/biops-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/biops.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/biops/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/bench-test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/bench-test4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats1.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats2.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats3.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/birats4.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/birats/test4.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/cervix-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/cervix-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/cervix.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/cervix/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/dugongs.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/dugongs/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/eyes-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/eyes-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/eyes.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/eyes.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/eyes2.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/notest1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/eyes/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/hearts-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/hearts-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/hearts.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/hearts.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/hearts/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/bench.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/ice-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/ice-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/icear.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/ice/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/bench-test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/jaw-constant.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/jaw-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/jaw-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/jaw-linear.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/jaw-quadratic.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/jaw/test3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/bench-test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/mvotree-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/mvotree-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/mvotree.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/orange-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/orange-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/otree.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/otree.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/otree.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/test2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/orange/test2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/pigs-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/pigs-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/pigs.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/pigs/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/bench-test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/schools-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/schools-inits.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/schools.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/schools.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/test.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/test1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/schools/test1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/ReadMe
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/bench-test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/bench-test4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/notest1.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/notest2.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-data.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits1.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits2.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant-inits4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/stagnant2.bug
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/test3.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/test3.cmd
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/test4.R
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vol2/stagnant/test4.cmd
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/stagnant
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/schools
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/pigs
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/orange
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/jaw
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/ice
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/hearts
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/eyes
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/dugongs
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/cervix
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/birats
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/biops
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/beetles
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/asia
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/alli
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2/air
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol2
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/seeds
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/salm
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/rats
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/pump
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/oxford
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/mice
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/lsat
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/litters
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/line
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/leuk
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/kidney
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/inhaler
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/equiv
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/epil
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/dyes
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/bones
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1/blocker
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/vol1
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/R
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
 @dirrm lib/JAGS/modules-%%MODULEVERSION%%
 @dirrm lib/JAGS
 @dirrm include/JAGS/util