update math/R to 2.15.3, and adjust dependent ports

40 files changed, 52 insertions, 32 deletions

diff --git a/math/R-cran-Formula/Makefile b/math/R-cran-Formula/Makefile
index 4b2cdbed5e97..a389de255cb9 100644
--- a/math/R-cran-Formula/Makefile
+++ b/math/R-cran-Formula/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	Formula
 DISTVERSION=	1.1-0
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-KFAS/Makefile b/math/R-cran-KFAS/Makefile
index 83aa9002fa39..c3d452f3d62d 100644
--- a/math/R-cran-KFAS/Makefile
+++ b/math/R-cran-KFAS/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	KFAS
 PORTVERSION=	0.9.11
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-LearnBayes/Makefile b/math/R-cran-LearnBayes/Makefile
index ddeac367b216..f04c0c123954 100644
--- a/math/R-cran-LearnBayes/Makefile
+++ b/math/R-cran-LearnBayes/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	LearnBayes
 PORTVERSION=	2.12
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-MCMCpack/Makefile b/math/R-cran-MCMCpack/Makefile
index 49c53c1c9b74..52e27c16772c 100644
--- a/math/R-cran-MCMCpack/Makefile
+++ b/math/R-cran-MCMCpack/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	MCMCpack
 DISTVERSION=	1.2-4
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-RHmm/Makefile b/math/R-cran-RHmm/Makefile
index 2ac3ead1d490..dd111fde9ce3 100644
--- a/math/R-cran-RHmm/Makefile
+++ b/math/R-cran-RHmm/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	RHmm
 PORTVERSION=	2.0.2
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-RSvgDevice/Makefile b/math/R-cran-RSvgDevice/Makefile
index 4e5736aea998..69a84dee5713 100644
--- a/math/R-cran-RSvgDevice/Makefile
+++ b/math/R-cran-RSvgDevice/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	RSvgDevice
 PORTVERSION=	0.6.4.2
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-SuppDists/Makefile b/math/R-cran-SuppDists/Makefile
index d6269f46a1d2..757f110e3013 100644
--- a/math/R-cran-SuppDists/Makefile
+++ b/math/R-cran-SuppDists/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	SuppDists
 DISTVERSION=	1.1-8
-PORTREVISION=	8
+PORTREVISION=	9
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_CRAN} \
 		http://r.research.att.com/benchmarks/:benchmark \
diff --git a/math/R-cran-Zelig/Makefile b/math/R-cran-Zelig/Makefile
index 1fa89f08142e..e79341f0b470 100644
--- a/math/R-cran-Zelig/Makefile
+++ b/math/R-cran-Zelig/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Zelig
 DISTVERSION=	4.1-1
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-bdsmatrix/Makefile b/math/R-cran-bdsmatrix/Makefile
index 1c599b6288e9..9ad827b196d7 100644
--- a/math/R-cran-bdsmatrix/Makefile
+++ b/math/R-cran-bdsmatrix/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	bdsmatrix
 PORTVERSION=	1.3
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-car/Makefile b/math/R-cran-car/Makefile
index aa0c9e308002..e9d019341c1d 100644
--- a/math/R-cran-car/Makefile
+++ b/math/R-cran-car/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	car
 DISTVERSION=	2.0-16
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-coda/Makefile b/math/R-cran-coda/Makefile
index d50e9ab94167..a77df8472d4d 100644
--- a/math/R-cran-coda/Makefile
+++ b/math/R-cran-coda/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	coda
 DISTVERSION=	0.16-1
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-deldir/Makefile b/math/R-cran-deldir/Makefile
index 88f67981b355..b06c4f9eb1de 100644
--- a/math/R-cran-deldir/Makefile
+++ b/math/R-cran-deldir/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	deldir
 DISTVERSION=	0.0-21
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-dlmodeler/Makefile b/math/R-cran-dlmodeler/Makefile
index 2898014dce93..990c14f90382 100644
--- a/math/R-cran-dlmodeler/Makefile
+++ b/math/R-cran-dlmodeler/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	dlmodeler
 DISTVERSION=	1.2-1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-gpclib/Makefile b/math/R-cran-gpclib/Makefile
index 42e4c6910f62..a8f98a4179af 100644
--- a/math/R-cran-gpclib/Makefile
+++ b/math/R-cran-gpclib/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	gpclib
 DISTVERSION=	1.5-3
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-gtable/Makefile b/math/R-cran-gtable/Makefile
index 71616565adf9..74c9dab36d48 100644
--- a/math/R-cran-gtable/Makefile
+++ b/math/R-cran-gtable/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	gtable
 PORTVERSION=	0.1.2
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-igraph/Makefile b/math/R-cran-igraph/Makefile
index 16cf5ca1ebdd..13deb26fdea2 100644
--- a/math/R-cran-igraph/Makefile
+++ b/math/R-cran-igraph/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	igraph
 DISTVERSION=	0.6.5-1
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-inline/Makefile b/math/R-cran-inline/Makefile
index af284410b105..fe990984406e 100644
--- a/math/R-cran-inline/Makefile
+++ b/math/R-cran-inline/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	inline
 PORTVERSION=	0.3.10
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-labeling/Makefile b/math/R-cran-labeling/Makefile
index ff1fc3d150dd..4c9b72a47dc0 100644
--- a/math/R-cran-labeling/Makefile
+++ b/math/R-cran-labeling/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	labeling
 PORTVERSION=	0.1
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-memisc/Makefile b/math/R-cran-memisc/Makefile
index b28e0f2ffbda..fad06cf8dfb8 100644
--- a/math/R-cran-memisc/Makefile
+++ b/math/R-cran-memisc/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	memisc
 DISTVERSION=	0.96-3
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-mvtnorm/Makefile b/math/R-cran-mvtnorm/Makefile
index 503ab8e907a3..2a327bb16412 100644
--- a/math/R-cran-mvtnorm/Makefile
+++ b/math/R-cran-mvtnorm/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	mvtnorm
 PORTVERSION=	0.9.96
-PORTREVISION=	9
+PORTREVISION=	10
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION:C/\./-/g:C/-/\./1}
 
diff --git a/math/R-cran-nnls/Makefile b/math/R-cran-nnls/Makefile
index 027354b0b8b8..508c3b9c5201 100644
--- a/math/R-cran-nnls/Makefile
+++ b/math/R-cran-nnls/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	nnls
 PORTVERSION=	1.4
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-psych/Makefile b/math/R-cran-psych/Makefile
index 92900d92b0a4..dc5c5aa6c8af 100644
--- a/math/R-cran-psych/Makefile
+++ b/math/R-cran-psych/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	psych
 PORTVERSION=	1.2.1
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	math science
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
diff --git a/math/R-cran-quadprog/Makefile b/math/R-cran-quadprog/Makefile
index 2e83bd355924..0a515846d76f 100644
--- a/math/R-cran-quadprog/Makefile
+++ b/math/R-cran-quadprog/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	quadprog
 DISTVERSION=	1.5-4
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-sandwich/Makefile b/math/R-cran-sandwich/Makefile
index 35a1067287ed..382ab19bd99d 100644
--- a/math/R-cran-sandwich/Makefile
+++ b/math/R-cran-sandwich/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	sandwich
 DISTVERSION=	2.2-9
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-sm/Makefile b/math/R-cran-sm/Makefile
index 52555f815204..91630d7ffd84 100644
--- a/math/R-cran-sm/Makefile
+++ b/math/R-cran-sm/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	sm
 DISTVERSION=	2.2-4.1
-PORTREVISION=	9
+PORTREVISION=	10
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-sp/Makefile b/math/R-cran-sp/Makefile
index c2ecec28aac8..12aa24732292 100644
--- a/math/R-cran-sp/Makefile
+++ b/math/R-cran-sp/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	sp
 DISTVERSION=	1.0-5
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-spdep/Makefile b/math/R-cran-spdep/Makefile
index e9e3d022230b..7e3844d65809 100644
--- a/math/R-cran-spdep/Makefile
+++ b/math/R-cran-spdep/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	spdep
 DISTVERSION=	0.5-56
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-stabledist/Makefile b/math/R-cran-stabledist/Makefile
index 62f0c606d107..dd6d30eaf09e 100644
--- a/math/R-cran-stabledist/Makefile
+++ b/math/R-cran-stabledist/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	stabledist
 DISTVERSION=	0.6-5
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-xts/Makefile b/math/R-cran-xts/Makefile
index 1eabbd4cd596..0c2e24acb70c 100644
--- a/math/R-cran-xts/Makefile
+++ b/math/R-cran-xts/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	xts
 DISTVERSION=	0.9-3
+PORTREVISION=	1
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R-cran-zoo/Makefile b/math/R-cran-zoo/Makefile
index 97a0c27b2c89..23b920b4f66e 100644
--- a/math/R-cran-zoo/Makefile
+++ b/math/R-cran-zoo/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	zoo
 DISTVERSION=	1.7-9
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 DISTNAME=	${PORTNAME}_${DISTVERSION}
 
diff --git a/math/R/Makefile b/math/R/Makefile
index 42ba79b94524..234d495e70fc 100644
--- a/math/R/Makefile
+++ b/math/R/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME?=	R
-PORTVERSION=	2.15.2
+PORTVERSION=	2.15.3
 CATEGORIES=	math lang
 MASTER_SITES=	http://cran.r-project.org/src/base/R-2/ \
 		ftp://cran.r-project.org/pub/R/src/base/R-2/ \
diff --git a/math/R/distinfo b/math/R/distinfo
index fad9cc36359d..8a5ff735289e 100644
--- a/math/R/distinfo
+++ b/math/R/distinfo
@@ -1,2 +1,2 @@
-SHA256 (R-2.15.2.tar.gz) = 292837ae259b7668509b8a5d4ec8be0aa50c327cfe7a534bac419b4ca766d66d
-SIZE (R-2.15.2.tar.gz) = 24338934
+SHA256 (R-2.15.3.tar.gz) = c583a38f8dad3bc012c08116f4ba1eb2182cadfad4b0f8d7bd3cdba24bc255d6
+SIZE (R-2.15.3.tar.gz) = 25409925
diff --git a/math/R/pkg-plist b/math/R/pkg-plist
index 134f5d8bfef2..dd58f67ee34a 100644
--- a/math/R/pkg-plist
+++ b/math/R/pkg-plist
@@ -206,7 +206,6 @@ lib/R/library/Matrix/doc/Intro2Matrix.pdf
 lib/R/library/Matrix/doc/Introduction.R
 lib/R/library/Matrix/doc/Introduction.Rnw
 lib/R/library/Matrix/doc/Introduction.pdf
-lib/R/library/Matrix/doc/Matrix.bib
 lib/R/library/Matrix/doc/SuiteSparse/AMD.txt
 lib/R/library/Matrix/doc/SuiteSparse/CHOLMOD.txt
 lib/R/library/Matrix/doc/SuiteSparse/COLAMD.txt
@@ -429,6 +428,7 @@ lib/R/library/datasets/help/datasets.rdx
 lib/R/library/datasets/help/paths.rds
 lib/R/library/datasets/html/00Index.html
 lib/R/library/datasets/html/R.css
+lib/R/library/foreign/COPYRIGHTS
 lib/R/library/foreign/DESCRIPTION
 lib/R/library/foreign/INDEX
 lib/R/library/foreign/LICENCE
@@ -914,12 +914,14 @@ lib/R/library/parallel/libs/parallel.so
 %%NLS%%lib/R/library/parallel/po/zh_CN/LC_MESSAGES/parallel.mo
 lib/R/library/rpart/DESCRIPTION
 lib/R/library/rpart/INDEX
+lib/R/library/rpart/NEWS.Rd
 lib/R/library/rpart/Meta/Rd.rds
 lib/R/library/rpart/Meta/data.rds
 lib/R/library/rpart/Meta/hsearch.rds
 lib/R/library/rpart/Meta/links.rds
 lib/R/library/rpart/Meta/nsInfo.rds
 lib/R/library/rpart/Meta/package.rds
+lib/R/library/rpart/Meta/vignette.rds
 lib/R/library/rpart/NAMESPACE
 lib/R/library/rpart/R/rpart
 lib/R/library/rpart/R/rpart.rdb
@@ -927,6 +929,13 @@ lib/R/library/rpart/R/rpart.rdx
 lib/R/library/rpart/data/Rdata.rdb
 lib/R/library/rpart/data/Rdata.rds
 lib/R/library/rpart/data/Rdata.rdx
+lib/R/library/rpart/doc/index.html
+lib/R/library/rpart/doc/longintro.R
+lib/R/library/rpart/doc/longintro.Rnw
+lib/R/library/rpart/doc/longintro.pdf
+lib/R/library/rpart/doc/usercode.R
+lib/R/library/rpart/doc/usercode.Rnw
+lib/R/library/rpart/doc/usercode.pdf
 lib/R/library/rpart/help/AnIndex
 lib/R/library/rpart/help/aliases.rds
 lib/R/library/rpart/help/paths.rds
@@ -1133,6 +1142,7 @@ lib/R/library/survival/data/Rdata.rdb
 lib/R/library/survival/data/Rdata.rds
 lib/R/library/survival/data/Rdata.rdx
 lib/R/library/survival/doc/index.html
+lib/R/library/survival/doc/sourcecode.pdf
 lib/R/library/survival/doc/timedep.R
 lib/R/library/survival/doc/timedep.Rnw
 lib/R/library/survival/doc/timedep.pdf
@@ -1624,6 +1634,7 @@ lib/R/share/texmf/tex/latex/upquote.sty
 @dirrm lib/R/library/rpart/libs
 @dirrm lib/R/library/rpart/html
 @dirrm lib/R/library/rpart/help
+@dirrm lib/R/library/rpart/doc
 @dirrm lib/R/library/rpart/data
 @dirrm lib/R/library/rpart/R
 @dirrm lib/R/library/rpart/Meta
diff --git a/math/ess/Makefile b/math/ess/Makefile
index 16a8c224eece..16a336ebeffa 100644
--- a/math/ess/Makefile
+++ b/math/ess/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	ess
 DISTVERSION=	12.09-2
+PORTREVISION=	1
 CATEGORIES=	math
 MASTER_SITES=	http://ess.r-project.org/downloads/ess/
 EXTRACT_SUFX=	.tgz
diff --git a/math/p5-Statistics-R/Makefile b/math/p5-Statistics-R/Makefile
index 2ebda27d928c..cd05bd1fb8f7 100644
--- a/math/p5-Statistics-R/Makefile
+++ b/math/p5-Statistics-R/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Statistics-R
 PORTVERSION=	0.31
+PORTREVISION=	1
 CATEGORIES=	math perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:FANGLY
diff --git a/math/rkward-kde4/Makefile b/math/rkward-kde4/Makefile
index ac9f5f450d28..d1fdac2a2efa 100644
--- a/math/rkward-kde4/Makefile
+++ b/math/rkward-kde4/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	rkward
 PORTVERSION=	0.6.0
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	math
 MASTER_SITES=	SF/${PORTNAME}/Current_Stable_Releases
 PKGNAMESUFFIX=	-kde4
diff --git a/math/rkward/Makefile b/math/rkward/Makefile
index 7bc345818a3d..015e162e9f58 100644
--- a/math/rkward/Makefile
+++ b/math/rkward/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	rkward
 DISTVERSION=	0.4.9a
-PORTREVISION=	18
+PORTREVISION=	19
 PORTEPOCH=	3
 CATEGORIES=	math
 MASTER_SITES=	SF/${PORTNAME}/Historical_Releases/0.4.x_and_earlier/0.4.9a%20%28KDE3%29
diff --git a/math/rpy/Makefile b/math/rpy/Makefile
index 000e275f6a87..2fb09b182c96 100644
--- a/math/rpy/Makefile
+++ b/math/rpy/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	rpy
 PORTVERSION=	1.0.3
-PORTREVISION=	26
+PORTREVISION=	27
 CATEGORIES=	math
 MASTER_SITES=	SF
 
diff --git a/math/rpy/pkg-plist b/math/rpy/pkg-plist
index 9f27b53a1207..2e3ef74a3e8e 100644
--- a/math/rpy/pkg-plist
+++ b/math/rpy/pkg-plist
@@ -1,4 +1,4 @@
-%%PYTHON_SITELIBDIR%%/_rpy2152.so
+%%PYTHON_SITELIBDIR%%/_rpy2153.so
 %%PYTHON_SITELIBDIR%%/rpy.py
 %%PYTHON_SITELIBDIR%%/rpy.pyc
 %%PYTHON_SITELIBDIR%%/rpy.pyo
diff --git a/math/rpy2/Makefile b/math/rpy2/Makefile
index a189679bbb0f..072e45d20cb0 100644
--- a/math/rpy2/Makefile
+++ b/math/rpy2/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	rpy2
 PORTVERSION=	2.2.6
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	math
 MASTER_SITES=	CHEESESHOP \
 		SF